The Seeds of Worlds
by Blades of Chance
Summary: Adam and Lilith. Two ancients Seeds which crashed on the Earth. They are not the only ones. With the world ravaged by the effects of Second Impact and a War between Life and Knowledge, the creations of Adams and Lilith, such secrets are bound to reappear. It seemed like things are more complicated. For Shinji a question exists. Why is there a voice in his head?
1. Prologue

**I just made another story like it is no big deal. Which It kind if isn't. I have to many of them. Well, I am too late.**

 **As for how this story came to be. In the back lore of the series, it is stated that there were more seeds besides Adam and Lilith. Most of which likely ended up on their world without a problem. Seeing how no one has yet to do anything with it I figured why not?**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

 _Yui looked up as everyone frantically tried to do something about the deteriorating situation. They removed the spear within Adam and soon after the seemingly dead giant awoke. The base they built was torn apart as the Angel walked out and unleashed its powers. They tried to use the spear against it._

 _The result was that it brought it's spear to them and now it seemed like it was doing something that was destroying everything around them. The sky light up as massive wings made of light shot up into the atmosphere. "We gotta get out of here!"_

 _Yui turned to her colleague as everyone was frantically trying to evacuate. Thing is she didn't know if they could. The ground shook as Adam stabbed his spear into the ground as the ice and rocks were sent flying into the air along with many of the unwilling people. A groan escaped Yui as she pulled herself up and feel on the cold ice. Her leg was broken and she was bleeding. 'Gendo,' She turned around and looked at Adam. The sky above him pulsed red as Yui felt fear within her heart. 'W-we're going to die.'_

 _Her vision blurred as she fell in and out of consciousness. She thought she saw a light in the dark sky than an outline of something fighting Adam. An ear-splitting screen echoed across her ears. When she finally came to the sky was slowly snowing as the ground around her flowed with an unknown substance. 'I-I'm I dead?'_

 _After a second she realized that she wasn't dead. Looking up she saw that a spear was embedded into the ground before her with remains of the Geofront blasted around. A sound caught her attention as she turned to her side finding a figure lying in the ground. Its legs and it's left arm was torn off with a strange blood substance flowing from its wounds. It turned its head to her as Yui saw that it had three eyes, emphasis on had, the one on its right side was missing._

 _Yui looked into its eyes as it raised its remaining hand to her and touched her shoulder. A flash of light consumed them both before Yui fell unconscious again._

* * *

Yui awoke from her desk with a bit of a fright. It was that dream again. It was only a few months since Second Impact happened. When the first Angel Adam whipped out a third of the world's population. Wars were raging and already more were dying. ' _And now an organization is moving to wipe out the rest of humanity.'_

Said group included her father of all people. It's from him that she learned about the fact that Adam awakening caused the Angels that had lay dormant within the world. All save for one which they found in the second Geofront. ' _Seed-ship of Knowledge.'_

There was that voice again. Yui heard it ever since that day. She had no idea how it came about as there was nothing wrong with her. Yet, however, it constantly told her things that seemed to all be right and then some. It explained to them that both Lilith and Adam shouldn't be on this world. They also noted how the plan to create something to fight the Angels was just playing into the hands of her father and his friends.

' _It's not like I have anything else I can hope to do!'_ Maybe the stress was starting to get to her. Whatever the case it wasn't like she could do anything else to stop the whole thing from happening.

Getting out of her room she saw Kyoko crying over the phone. Her relationship with her husband was disintegrating as the days went on. "Aufstand in der Hölle, du Bastard!" Hanging up Kyoko pulled off her wedding ring and tossed it with all her might. "Fine if he doesn't want to be married then screw him."

Kyoko held her head down as tears fell from her eyes. Yui knew that Kyoko was thinking of having a child and hearing that her husband was leaving her wasn't what she wanted to hear. ' _An opportunity,'_ Yui heard the voice yet again. ' _You can derail the plans of your father.'_

Call her crazy but at this point, she decided to entertain the voice in her head. She might be going crazy but anyway to screw with their plans was one she was willing to do. ' _What are you thinking about?'_

* * *

Yui finished her latest project as she hoped that this would go as she had hoped. She already had one success with Kyoko even committed on how Asuka was perfectly healthy and acting like any other child her age. ' _As naturally as she could be given her origins.'_ The voice told her before it disappeared that she should find more ways to subvert the plans. That was what both this and her greatest project was for. ' _I just hope Gendo can understand.'_

Walking out of the lab she turned off the lights. With any luck, the tank should develop the second key to stopping the old men. As she walked out she saw her son Shinji playing with a toy that one of staff had given him. For a second looking at him, she saw that injured being that was next to her.

"Ma'am are you there?" She was pulled from the vision as one of the staff waved her hand in front of her. How long was she just standing there? "Ma'am we managed to get the first success should we begin fitting it?"

That was surprising news to hear. For a moment she heard the voice's warnings despite it not being in her head anymore. The Evangelion would be without a soul and would demand one from whoever tried to pilot it. This made her want to hesitant as whoever would be sent as a figurative sacrifice. "Go ahead but do not have anyone attempt at testing it until my say."

Now a question arises on what she was going to do about the problem of it demanding a soul. Her first idea was to send someone who won't be forgotten but she quickly realized that it was her upbringing talking. Furthermore, they were hoping for that as it made their plans easier. ' _There is always the risk that they would figure out how what I did and take actions to undo all I did.'_

On another hand, there was a chance for her to make sure that never happened. Although if she did that then that would leave Gendo and Shinji alone. After considering it for several minutes Yui knew what she was going to do. She found her husband looking over some of the designs she had. "Gendo mind if we talk?"

He turned to her with a neutral look on his face. It soon morphed into a small smile. "What is honey?"

Yui took a deep breath. He wasn't going to understand what she meant by what she was going to tell him. At least not until it was too late. "Promise me that if anything happens that you will watch over Shinji."

Confusion firmed on his face at this. "What brought this about?"

Just as Yui expected and it hurt her to not tell him everything out of fear for them both. Still, it was better this way. "I am thinking of taking the rest run and if anything happens I want you to promise me that you would take care of him."

"Don't worry I'm sure nothing would happen and if so," He placed his hand on her shoulder with a smile on his face. "I promise to watch out for him."

* * *

Gendo looked at himself within Yui's now his office. The photo of her looking back at him as he slammed his hand into his desk. The images gaze taunting him oh so much. "I'm sorry I just can't be a parent not with everything that we both know is going down!"

It was only made months since the tragedy were Yui had gotten absorbed into the Evangelion unit. Gendo had left Shinji with his uncle, ignoring his wife's wishes, all because of what he found out in her notes. The expedition to Antarctica, the truth of Second Impact, and the plans of SEELE. Strangely enough two pages were torn out when dealing with around the time that Kyoko husband broke up with her. ' _If only she hadn't been driven mad then I could know what it was that was so important.'_

Taking the picture into his hand he put it face down face first on his desk. He knew that he could find a way to use SEELE's plans against them. A way to save his wife and all of humanity. One of the keys was in the girl that his wife was creating. The notes he had said that she was putting Lilith's soul into it but beyond that nothing else. "Rei is the key to everything."

He was a bit unsettled by her questions. Supposedly she kept waking up talking about a woman muttering nonsense. Other times she spoke of her having visions of training to pilot. The room to his office was tossed open as one of the security came racing in. "Sir, Doctor Akagi throw herself off the catwalk and Rei isn't breathing!"

It took him a few moments to realize what just happened. He wondered why she did this. Naoko was close to a mental breakdown but still how did this happen? ' _Wait, I was talking to myself and Rei walked in…'_ He wanted to facepalm in annoyance at this. ' _I need to watch what I say around her.'_

It looked like it was time to collect her soul and get her out of the Reiquarium. With any look, this should be the only issue that this brings him.

* * *

Asuka awoke as her eyes adjusted to the light. The young girl immediately shot up as she placed her hands on her neck. She took several deep breaths as she found that she wasn't choking as she had thought. ' _What happened?'_

"Your up," The young girl turned her head as one of the bases doctor's. "You gave us quite the fright when you suddenly started to yell that you were choking and then fainted on us." He did leave out that she had entered into a coma and nearly seemed to have died on them. ' _How did this even happen?'_

The little girl looked at her hands. Asuka had felt like she had just died. Yet, here she was alive. She looked at the mirror next to her. The redhead stared into it as her red eyes looked back.

* * *

 _The heat was everywhere. Lava boiled from the barely formed crust. Overhead two newly forming moons orbited the planet. The light of two young stars glowed on the world. Finally waiting just overhead the ship that brought it here waiting for its command._

 _The primordial wind blew past it. The world was raw and full of potential. It was time to act. Stabbing the spear it had into the planet the object hanging overhead seemed to open up. Suddenly comets and asteroids floating around the system started to smash into the planet. The sky started to darken as clouds formed heavy with water._

 _Gripping the spear in hand a pulse came through it as the lava cooled across the planet. Rain fell from the clouds overhead as slowly lakes and primordial seas formed all around it. Pulling the spear from the crust it brought the tip to its hands and cut its palm. Holding it over drips of its blood-like substance fell into the water as lightning arced overhead._

 _The next image showed the newly been world as the being stood watching as the history passed. The world going from near lifeless to a lush, if cold world. A few needed alteration was required to make sure things moved as they wished._

 _The last few images were of cities forming up before another jump happened. This time it was over the earth. At the south pole of the planet, a dark pulse was spread out. The next image was it clashing with a white giant. It spoke in annoyance as the two spears hit each other. "You are not their progenitor!"_

" _And you are not Lilith!"_

* * *

Shinji awoke as he stared at the ceiling. That dream yet again. Every month he had the same one. Dreaming of a figure creating life on a far off world before cutting to fighting a giant. Beyond that nothing else. "Who is Lilith?"

That was a question that had never once been answered. Even still, he felt like he knew the answer to a question but that made no sense.

* * *

 **Shinji trust me you have no idea. Anyway, as you can guess the seed that came by the world was a Seed of Knowledge just like with Lilith. Its appearance has already changed a lot of things in this story. The questions will be answered as the story goes on. Until then I leave it at this.**

 **Cya all next time.**


	2. Chapter 1

**Here it is another chapter. Yeah, took me a bit to get it finished. I do hope you like it.**

 **Thank you knight7572, emotheextremo, and Scattershot98 for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

 _There was life on this world. Basic algae-like plants and something looking like insects but nothing else. A scan from the moon with the object in her hands was all that was needed to prove that it wasn't like them. This wasn't the world that she had landed on. Three years flying through the void and already five failures. Taking off again it continued to search even if it was coming to the end of the expansion zone._

 _A year later as it was about to give up as it reached the edge of the zone. Until it picked up the broken mess of a radio wave. Decayed heavily from the background radiation of space it was the first sign of life. Sentient life the rarest form in the galaxy. Following the signal in a years time, it passed by a primitive probe flying off from a yellow star. Hope began to fill it as this could finally be where it was searching for._

 _When it landed on the moon it looked out and saw a world teeming with life. The lights of cities could be seen from the night side of the planet. Holding up its spear it had to confirm it. It's or rather her voice was heard as a feminine tone escaped her mouth. "Yes!" Excitement filled her at this. "Black Seed-ship confirmed!"_

 _It pointed the spear as it waited for communications to be set up. After a full hour passed its expression turned sour. Something wasn't right. That was when it saw the skies darkening and the wings if light shooting out from the south pole. Its eyes widened at the spear confirmed the activation of a White Seed-ship Terraforming device. "Two seeds landed on the same planet?!"_

 _Wasting no time she jumped off the moon and headed for the south pole._

* * *

Shinji opened his eyes again as he realized that the train had stopped. He held onto the letter from his father. On it was just one simple sentence was written. Come to Tokyo-3. That was it more than a decade and only now did he actually want to speak to him. ' _Talk about a terrible parent.'_

The fourteen-year-old boy looked around for a moment before he realized it was just that voice in his head. Ever since he started having these dreams he has been hearing it. A feminine voice that spoke within his head. After a while, he just stopped worrying about why he had it. ' _I've been hearing it a lot more lately.'_

At this rate, he might just be going crazy. Given he was going to his father who left him with his uncle after a decade in hopes of getting something close to parental approval, despite every rational part of him saying it was impossible, he might as well be. After wondering for a few minutes he overheard the sounds of emergency. Planes flew overhead as Shinji was left questioning why.

' _Is it an invasion?'_ The Second Impact Wars while having been done for over a decade still left a tense situation. Shinji couldn't think of anyone who would be attacking. Maybe it was just a test in case of war.

Walking to a pay phone Shinji put in a call to his father. ' _You know he likely not to call you if this is an emergency.'_ The voice was back and it seemed to state what he was thinking. ' _Assuming he actually does care about you at all.'_

The automatic messaging system came on informing him that they couldn't forward the call. It was just like

Putting the phone back Shinji pulled out the envelope that came with his letter. Someone named Misato Katsuragi. Shinji looked at the photo of her with an arrow pointing to her rather generous amount of cleavage. ' _You know she is rather beautiful,'_ Shinji had a blush after hearing the feminine voice within his head say that. ' _If only your gender wasn't as is.'_

He decided to ignore it as he continued to look out wondering where everyone was before hearing the sounds of explosions and artillery fire. In one of the buildings, he saw the reflection of a huge monster from the many windows. "Wh-what the hell?!"

' _So, they are starting to awake.'_ It's official he was crazy as he had no idea what it meant. Before he could take off and run he had to jump out if the way as a car came racing to him before opening the door to the front passenger seat.

"Sorry I'm late," The woman driving the car removed her sunglasses revealing that it was Misato. "Now get in!"

* * *

Gendo looked as the Japanese Strategic Self Defense Force, and the U.N. both took their chance to defeat the Angel. Fifteen years since Second Impact broke the world. Yui wrote about them coming in her notes. ' _The war begins just as you said.'_

Looking at the footage it was almost painful to watch. Everything they threw at the creature was just deflected by its A.T. field. The look on the military leaders was amusing all things considered. They had dismissed him and told him that they would take care of the Angel. He had told them so. "Damn it!" The leader of the Japanese forces was getting frustrated at the seemingly hopeless situation. "Screw it drop the N2 now!"

The other two commanders, both from the U.N. force, looked at him for a moment before coming to an agreement. The planes moved out of the way and the military forces pulled back as a rocket carrying the strongest weapon in the JSSDF arsenal was sent at the Angel. A massive explosion lite up the screen. It seemed that the weapon had done the trick. "Yes!" The celebration was cut short as when the feed returned it showed the Angel still standing.

"The Angel's A.T. field has extended itself the damage it sustained is regenerating." A small smirk formed on Gendo's face at this. The fools were told that they couldn't defeat the Angel.

Gendo just watched as the Commander tried to see if they could do anything. After being shot down for his last crazy idea. Now it was time for him to take control of a situation as he should have. "Gentlemen I believe that my case has been made," The three of them turned to him as he adjusted his glasses. "You can not take out the Angel without my forces."

A sigh escaped the JSSDF Commander. He had rather not allow an organization with no government oversight, and a lot of freedom from its U.N. oversight, deal with these things. Yet, they didn't have a choice. One of the U.N. representatives decided to speak up. "Very well if NERV can prove that it can then you will have sole authority for any future incidents."

The three of them saw themselves out. No further words were exchanged as Gendo continued to look at the Angel. "We are down a pilot you know," He turned to his Sub-Commander and former teacher Kozo Fuyutsuki. "Rei is too injured to pilot if you recall."

"I know and that is why Misato is getting our new pilot." Gendo returned to looking at the Angel.

"Oh yes, your son Shinji." It had been a long time since he had seen the boy. Kozo was always curious as to why he had left him with his brother.

At that moment Gendo recalled the promise that he gave his wife. A promise that he had failed to keep. For a moment he wondered how he could make amends to her and for him. ' _Perhaps I could order Rei to be with him?'_

* * *

Almost getting hit by an N2 explosion was not something Shinji had expected to ever happen to him. Then came learning about the real case of Second Impact. Surprisingly enough when he read it he felt like he had both known it but also that the report was terribly lacking in understanding. ' _At least the terraforming process was stopped before the worse could happen.'_

' _I know it must be going crazy because there is no way that I should believe that.'_ Thing is he had a feeling that all the voice had said was true. That the first Angel was attempting to terraform the world and failed but still caused Second Impact.

Misato stopped the car and turned to him. "Well, are you excited to see what your dad been working on?"

If he was honest he was still mad that he just left him. Sure he knew he was working on something but beyond that, his Uncle had no idea what. Shinji spoke almost a whisper as he figured that his father just wanted something from him. "Not really."

Having not heard him, or not heard what he said, Misato didn't comment on it. Instead, she pulled out a map of NERV which was given to her. The voice within Shinji's head was quick to pick it up. ' _I am guessing that she is new here and has gotten lost several times before.'_

That wasn't reassuring. Though looking at the map over her shoulder he could tell that the place was rather big and seemed to be built like a maze within the Geofront. ' _How did something like this even get built?'_

' _By digging out part of an ancient spaceship that crashed into the planet.'_ That sounded like a plot for a sci-fi franchise. Once again though he knew it as fact.

After wondering for a few minutes Misato led him to a room which had a large purple robot. Shinji looked at the thing as for a moment he recalled seeing something like it. A blueprint for a thing looking just like it. Followed by several giant corpses huddled together in a graveyard. The voice in his head spoke with a rather sober tone. ' _So, she actually did it giving up her own life over anyone else's.'_ Shinji felt like he didn't want to know what the voice was talking about.

"I see you didn't get lost this time," Misato turned as the head scientist of NERV, Ritsuko Akagi. She looked at Shinji noticing the similarities he had to Gendo. "So, this is the Commander's son the Third Child."

Shinji wondered why he was being called Third Child. Was this the reason that his father had decided to call him back? "He is," Speak of the devil and he will appear. Shinji turned to see his father walking up to him. "It's been a long time Shinji."

For more than a decade Shinji hadn't seen his father. Even now he didn't know what to feel as he looked at the man in front of him. In the end, he just spoke with mild annoyance. "Father."

Gendo adjusted his glasses as he looked at Eva-01. His wife was if her writings to be believed still vaguely aware of what was going on. Hopefully, he could convince Shinji to pilot Eva-01. "I will be brief I need you to pilot the giant robot."

His dad called him here after more than a decade in order to pilot a giant robot. He called his fourteen-year-old son to probably fight some monster within a giant robot. ' _Actually, it's fitted around an organic center so it would be more accurate to call it a cyborg.'_

He was going to figure out how the voice knew all of this. If it even was a voice that is. "You called me here just so that I would pilot your robot and fight that thing out there?" Shinji didn't know why he expected anything less from him. "Forget it I'm not piloting that thing!"

There wasn't a change in expression on Gendo's face. He knew that his son was likely to harbor anger at him. If he was being honest Gendo believed it was rather justified. Sadly he didn't have time to explain himself to his son. He turned over to Kozo. "Get Rei it looks like my son refuses to pilot."

Kozo seemed hesitant for just a moment before nodding. Misato looked at Gendo like he was crazy. Ritsuko had to make sure she heard that right. Shinji was confused until he saw Kozo wheeling in an injured girl on a hospital bed. ' _He can't seriously be thinking of letting her pilot the robo-cyborg in her condition.'_

Rei opened her unmanaged eye as Gendo walked over to her. This was deceitful, and while he could just have her soul put into another clone body, he rather not go through with that right now. "Two my son is useless I need you to pilot Eva-01."

The girl didn't complain and just gave a weak nod before trying to get out of her hospital bed. She immediately fell out and was caught by Shinji before she could hit the ground. She stared at him with her one eye while Shinji looked at her. A sense of familiarity came over him as suddenly both he and the voice spoke in his mind at the same time. ' _Lilith.'_

For a moment no words were said as Shinji picked her up and placed her back on the hospital bed. Turning to his father he gave him a cold look. Gendo looked back as he almost for a moment swear that his son's eyes turned a dark yellow. "I'll pilot but you haven't to promise me that you won't do that to her ever again."

That worked a lot better then he had expected. Although Gendo could have sworn Shinji's voice near the end had started to sound feminine. ' _It's probably nothing.'_ He adjusted his glasses before turning to Ritsuko. "Get Eva-01 ready for launch we have our pilot."

* * *

Gendo watched the recording again before once again realizing that he messed up when it came to Shinji. The first half of it was simply the Angel just toying with the untrained pilot. Then to both his shock and the Angels Eva-01 began to beat down on the Angel rather savagely. Gendo winced as he had a terrible feeling that Eva-01 was picturing him. ' _I just realized my wife is currently able to crush me in her hands.'_

When this all ends he is going to be in so much trouble. At least there was nothing physically wrong with Shinji this time. He made a note to get his son some training with a gun and self-defense. If this happens again he would only be digging himself deeper. Not like he wasn't already in a lot of crap as is with her.

With the video over there then came the issue of what to do about Shinji's living arrangements. Gendo kind of lived at the base as it is. Forcing Shinji to live here was out of the question. Misato had an apartment with two spare rooms. ' _Ritsuko commented that she did live in a mess of an apartment.'_

It was better than putting him in the one building that NERV owned above on the surface. Only Rei's room was even close to liveable and that was taking a very loose term of the word liveable. Even he is not dumb enough to realize that doing so would enrage Yui further. So left with these options he chose the lesser of three evils. The door to his office opened up as Kozo walked in with several old files and a dairy. "You know I went and retrieved the old designs that Kyoko had for Eva-00 at Ritsuko request and I stumbled on Kyoko's old diary before she had transferred over to the German branch."

His wife's old friend and colleague. Kyoko was possibly the only one, besides him, that he could see Yui telling about the notes that she had. For a moment he wandered back to the removed pages in his wife's journal. ' _What are the odds that it is in her diary?'_ Slim but if there was a chance he might as well take it. "I'll see to it that it gets delivered to her daughter."

Kozo gave him a nod before handing the diary over along with the key. As soon as his Sub-Commander was gone he unlocked the diary and looked through the pages. A violation of the privacy of Kyoko that it was he had to see if it was there. Finally, he landed on the pages he was looking for. After reading it he closed the diary and looked at the image of his wife on his desk. ' _You had a proof of concept for Rei it seems.'_

On one hand, it seemed like this complicated things. Rei was needed to return to Lilith in order to cause Third Impact as he envisioned it. Finding out that his wife made another vessel for part of Lilith's soul meant that plan would have to be thrown out the window. ' _Or perhaps not,'_ Depending on how he went about this he might be able to get both of them to perform Third Impact though how that would go about he was still unsure. ' _Asuka Langley Soryu.'_

He was going to to get her sent here as soon as possible. Gendo couldn't risk SEELE figuring out that his wife had done. He almost wondered how Rei would react to all of this. If the writings are to be believed then he wondered how she would react to meeting her half-sister.

* * *

Shinji saw himself in a dark room with a light appearing over him. For a moment he wondered how he got here and where here even was. "You are within your soul," The feminine voice from before was heard yet again as Shinji saw a chair. "Well, actually our soul."

In front of the chair was a woman. Her skin was purple her hair was both dark grey and light blue each on one side of her head. Her eyes had black sclera, dark yellow with cat-like pupils. A third eye rest on her forehead with yellow sclera and purple iris, and a red pupil. Out of her back were two large demonic wings. She wasn't wearing any clothes but it wasn't like it was hiding anything. She had almost the same anatomy as a doll. Still, her body was drop dead amazing with ample breasts almost the size of Misato's and a figure that was one most models would kill for.

Pushing away his teenage thoughts. Shinji caught sight of her fingernails which were more like claws as she motioned him to the seat in front of her. When she opened her mouth Shinji could see that in place of canines she instead had fangs. "Take a seat and I'll explain everything."

He stared at the being in front of him for a few moments before taking the seat. This was just so weird as he felt like he knew her and what is even stranger he felt like he was her. "Who…" He looked at the demonic looking lady, "Wh-what are you?"

The lady in front of him just looked at his confused expression before rolling her eyes. "As said before I am you or well if you want I am your past life, other self, and soul among other things," Around them the darkness gave way to show a broken purple figure touching his injured mother. "I transferred my soul after fighting the Seed of Life that ended up on your world in hopes of surviving while my body entered into an emergency healing state," Next showed Shinji being born. "When you were convinced you ended up becoming the vessel for my soul," She stopped and looked at him. "Well, now our soul."

Shinji looked at the woman or rather himself as the scene around them just turned into a star sky. She was supposed to be him? He paused as he realized where the voice in his head was coming from. "So, I'm some kind of what?" She called him a vessel for her soul so does that mean he wasn't a person. "An empty shell just to house you?

"No that is your body," She showed him, himself only with an emotionless look about him. "It is a shell to hold us," It was waved away from the two of them. "You are apart of me a separate personality within the realm of my soul as such if you want to get technical you can say you are and I are two parts of a greater whole."

Silence came over them as Shinji disgusted what he had just learned. The being in front of him was himself. That made him question if he should consider himself a boy? "Where did you come from?"

The lady stopped wondering how to explain this to him. She could easily fill him with the knowledge but he wasn't that developed for it yet. As he was apart of herself she would rather not destroy him and damage herself. "Let me explain while using a tale," With a snap, they saw themselves in the galaxy. "Billions of years ago fourteen seeds were sent out into the galaxy by an ancient species known as the First Ancestral Race," Before them were fourteen orbs seven white and seven black. "Half of these were known as the Seeds of Life and the other half the Seeds of Knowledge, each one representing a fraction and philosophy of the First Ancestral Race," The seeds were then scattered around as Shinji watched them landing on world after world. "Each one had the tools to turn whole worlds into paradises of life and civilizations in a time where life was rare in the galaxy and even now complex life is a rarity."

Shinji watched as from each one the barren world was changed. He noticed that the worlds were the black seeds landed became similar to his own. Though the life forms did look strange and somewhat alien he could at least make out what they were when compared to animals and planets on earth. The worlds were the white ones landed were utterly alien. Strange crystals, floating gases housed in rocks, and honeycomb-like things were just some of the more mild creatures.

Two of the seeds, one black and the other white, continued to float before they both landed on a world together. The world soon turned into the earth as it is Post-Second Impact. "There was only one thing no world was allowed to have both seeds as just like it had done before with the First Ancestral Race," The image of the Angel long with military troops fighting it appeared before them. "The two would clash and the world would be driven into war at best and at worse," A dead planet was shown before Shinji.

All of this was true. Somehow he knew that this was all real and that he had once taken part in it. The dream of him staring out on a newly formed planet. A question arose on how they fit into all of this. "Alright, so what does this all have to do with you?"

"Oh, that's easy see me and the others like are God-like entities meant to both create the life on these new worlds, teach them, and a whole lot of other things," The images ceased as they were within the dark room with just the two of them seated across from each other. "I am a Seed of Knowledge much like Lilith the progenitor of humanity."

With everything said Shinji was starting to get an idea on everything. That thing that had attacked Tokyo-3 and that he had fought. It was from the Seed of Life the thing that caused Second Impact. The voice in his head was of a Seed of Knowledge that had fought it and was his soul. "Wait, what is your name?"

The lady in front of him actually looked surprised by this. Perhaps she had expected him to just know her name given he was her and she was him. Maybe it was an effect of him being a separate personality. She had a embarrass look on her face at this. "Oh, I guess I just assumed you knew my bad," She pointed at herself as she gave him a wink. "My name is Lucifer, but you can call me Lucy."

* * *

 **Shinji as a lesbian female Progenitor Angel within his head and as his soul. I am just going to add that issue on top of you know all the ones he is feeling right now. Also, the foreshadowing is out and I want to hear how you feel about my take on the new dynamic that the pilots will have. I think I just did something unique.**

 **Cya all next time.**


	3. Chapter 2

**I am back with another chapter. I think I might need to update another. Anyway, on with the new chapter.**

 **Thank you** **c0l0r-bl1nd n355, Scattershot98, emotheextremo, and Kaze** **for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Grainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

An unfamiliar ceiling greeted Shinji as he opened his eyes. For a moment he wondered if all of that was a dream. Perhaps he was just imagining things. A sexy monster girl was within his soul did sound like something a teenage mind would think up. ' _You do know how to flatter a girl,'_ A naughty giggle was heard echoing in his head. ' _You are really naughty you know trying to hit on yourself.'_

As soon as the voice, no Lucy said those words he knew it was real. He actually did have her in his soul, well she was his soul, and everything she told him was real. ' _I am going to have a lot to think about.'_

Lucy left him to his thoughts as Shinji weighed his options and what he had. Right now it looked like he had basically been drafted into a war by his father. Shinji had expected that there was a catch but this was a too much. Now, he discovered that he had the soul of an ancient God-like entity, who happened to be of the same kind of thing that spawned humanity, and said entity was female. "When did my life turn into this?"

' _Sorry, but my defense I wasn't expecting to get nearly killed trying to stop planetary genocide!'_ Right, that part wasn't Lucy's fault. From what she told him the Seeds of Life and Knowledge were not supposed to end up on the same world. ' _Besides I didn't expect this to happen when I set off in search of my beloved.'_

Before Shinji could ask a bunch of follow up questions about this Misato walked in wearing a different outfit from before. Shinji wondered why she had decided to change. "Shinji you're awake."

She seemed rather surprised by this. Shinji looked at a clock overhead and saw that it was ten twenty-five. Had he been asleep for much of the afternoon? "How long was I out?"

"Oh about three days," Misato's answer caused Shinji shit up in surprise at this. He had been unconscious for three days! "Hey, chin up you won't be staying in here for long," She gave him a smile and a wink. "I'll be moving in with me."

Shinji didn't know what to say to that. Lucy, however, was a different story. ' _I think your father just did this because he doesn't have a place for you,'_ She stopped as she realized how terrible that sounded. ' _I am starting to understand why you don't think he loves you.'_

* * *

Rei stared at the ceiling in the medical ward without much of a care. She had heard about the Third Child defeating the Angel having piloted the Evangelion after seeing her in her current state. Strangely she had a vague sense that this wasn't the First time they had met each other. ' _Perhaps it was in my previous incarnation?'_

It had been a long time since then. It could be she had forgotten about him or an incomplete memory transfer. Thinking about it she dismissed it as according to what she remembered the Commander hadn't seen his son in over a decade, just before her first incarnation was allowed to walk around, so that couldn't be the case. Rei was pulled from her thoughts as she saw the Commander out the corner of her eye.

Gendo held Kyoko's diary in his hands. He had read the few passages about Asuka that Kyoko had written in. Call him curious but he had to see if there was anything unusual from the child to get something of an idea. "Rei it has come to my attention that you are not the only one of your kind," He handed her the diary and the page that he had marked. "It appears that you have a half-sister and I am doing all I can in order to make sure that she is transferred her as soon as possible."

Rei read over the notes with a tiny hint of surprise. The commander's wife had taken cells from her friend Kyoko and mixed in DNA from Lilith. According to this, she did state that she used a portion of Lilith's soul for the resulting baby. ' _I have a sibling.'_

This was a former thought to her. She didn't have anything of a family. At best she had genetic donors and a purpose to cause Third Impact the way Gendo wished. Reading that there was another person like her, one who shared both her DNA and her soul, made her want to meet them. ' _This also explains the strange feelings I have on occasion and those dreams.'_

She placed this book down as she thought about what this meant concerning her purpose. She knew since she was removed from the tank that her purpose was to cause Third Impact. To return to Lilith when everything was said and done and the last Angel had been defeated. Her sister, Asuka Langley Soryu, was now needed to complete that. A sister who had been made to give someone a daughter. A purpose that wasn't the same as her own. "What does this mean?"

"At best the scenario has to be altered to account for your sibling," That depend on if Asuka was easy to manipulate or if Rei could convince her. Given how her mother did die when she was young it was possible. "Also, I am moving you out of your apartment and having you live with Captain Katsuragi and my son."

Rei didn't question this as she gave him a nod. It was likely that he wanted the two pilots under one roof in order to make getting them easier. "Understood."

* * *

Misato's apartment was a complete mess. He had actually wondered how someone could even live in this place. Then he found out that she had a pet penguin, Pen Pen. A pet that was according to Misato was far more intelligent than normal thanks to being genetically altered. She also had two refrigerators one for Pen Pen to sleep in and another that had a lot of beer within it. ' _Let's see she drinks a lot of alcoholic substances, has rather revealing outfits, and her living space is a mess,'_ Lucy comment with a thoughtful expression. ' _I guess your father must have known about your need to keep things clean.'_

Shinji rolled his eyes at that. Like his old man knew anything about him. As he got rid of the last batch of beer cans he decided to take a break. Shinji's mind had a lot of questions. As he was cleaning he thought about why his father had called to get him to pilot a giant robot, why that girl seemed familiar, and even more about what Lucy was doing on earth when Second Impact happened.

" _I can answer two of them,'_ Of course, Lucy was still there with him. ' _The reason as to why he called you is probably due to your mother being the soul of Eva-01.'_

"Wait what?" That just sounded outlandish. Sure in the span of about three days he had learned the aliens are real, that all life on earth came from a God-like creature, and that he had one in his body as his soul. His mother being inside a giant robot, even one that was at the core organic, was just too much.

' _The Eva-01 has a soul and that is of your mother because if this it's likely only a handful of people could pilot it,'_ Lucy knew that Shinji was going to be in denial about this. It was the whole reason he had lost his memory of his early childhood. ' _As for why I was here?'_ There was a degree of embarrassment to her tone. ' _I kind of wanted to find Lilith because I may have…'_

Lucy didn't seem like she wanted to answer it but Shinji had an idea as to what it was. That was two questions answered although the last one was something that they both wondered. After thinking about any reason for it Lucy remembered what You had done for her friend. ' _She has part of Lilith's soul!'_

Shinji wondered if he heard that right. She was like him and had Lilith's soul within her? ' _How do you know that?'_

' _Because it's already happened before,'_ Lucy didn't know if this was a good thing or a bad thing. splitting up a soul had a variety of problems. Having two conscious beings with pieces of the same soul was bound to cause a bleeding effect.' _Your mother made a child for her friend Kyoko using said win and genes mixed with Lilith's own and then infused a part of Lilith's own soul.'_

Lucy showed him what she meant. In the images from what Lucy recalled was Yui creating a child for her heartbroken friend. This noble intention had another motive behind it. By pointing part of Lilith's soul into the child Yui hoped to prevent Third Impact from coming into being. ' _Are you saying that the girl we just met is the same?'_

Lucy, if she could, would have shaken her head at this. She knew that the one that Yui had made for Kyoko was a redhead and this girl had ice blue colored hair. This had to be another girl grown and infused with another part of Lilith's soul. ' _This is a different girl.'_

The door opened up as Misato walked into the apartment with a box in her arms. "Hey, Shinji could you help me clean out the other room?" Misato put the box down as Shinji saw a bunch of books and underwear within it. Underwear for a girl around his age. "We'll be having another roommate living with us."

He looked at her with a questioning look. "Who?"

"Oh, Rei would be moving in with us."

* * *

Asuka Langley Soryu looked at herself in the mirror as she moved her right arm. The phantom sensation of it being broken still lingering as she knew that wasn't the case. For the last few days, she had felt this without knowing why it was. The doctors had not the faintest clue. Even the local metaphysical specialists couldn't give a straight answer. ' _It's not as weird as the dreams I am having.'_

In them, she is in a room with a giant of white nailed at a cross off to the side. The floor below her was filled with LCL fluid and despite it being liquid she was standing on it like it was solid. In front of her was an albino ice blue haired girl with red eyes just like her own. The two would stare at each other. When one moved a limb the other would mirror it with there own. Asuka reached out to touch her and every time the dream would end before they could touch.

Walking out into the cage housing Eva-02 the redhead saw several of the NERV German branch arguing. Asuka was going to ignore it when one of them yelled in disbelief for her to hear. "He wants us to hand over both our pilot and our Evangelion Unit why?!"

Asuka turned her attention as she wondered if she heard that right. There was only a few who could demand her Evangelion and it's pilot. The U.N. Forces and other NERV branches came to mind. Even then she didn't think that anyone here would just willingly give up one of only four Evangelions in the world. "Yes, and the thing s I think the U.N. is backing him in this."

"Oh great they get beat up once and they are already doing whatever he wants," That was something she overheard the other day ago. An Angel had attacked Tokyo-3 and the JSSDF tried to stop it. They failed and then the newest pilot, the Third Child, took it on and killed it.

She was a bit annoyed that some rookie pilot got to fight in their Evangelion while she was stuck with continuing to practice for a fight instead of having one. She had been doing this the longest out of any other pilot as the only one even came close was the First Child and she still had years over them. "That's it then Eva-02 is going to Japan then?"

There was a nod from the person who broke the news. "Correct the U.N. fleet will be coming by to pick up the Evangelion and transfer it over while Asuka will be flown to Japan by the end of the week."

* * *

Shinji looked at his room as he sat on his bed. Misato had ordered takeout and after both, it and a few beers had passed out on the couch. He had moved her to her bed before returning to his own. The room next door was going to be for Rei when she got out of NERV's infirmary. ' _Tomorrow is my first day of school here.'_

He didn't have the best nor the worse memories when it came to school. He kind of just had school all things considered. Being something of an outcast. ' _You know I've been thinking,'_ Lucy seemed to appear out the corner of his eye. A trick of the mind to visualize the entity that shared the same soul with him. ' _Is it possible for us to use our powers even in the state we found ourselves in?'_

Lucy was talking about the abilities that she had. She had theorized that without the body of Lucifer they couldn't use any of them but as it was only a theory she had to be sure. ' _Wouldn't that set off some kind of alarm?'_

Shinji was worried about them possibly being attacked for being an Angel. That fact had crossed her mind a few times but Lucy figured she could trick the system. ' _This would be so much easier if we had our old body in front of us then we could just return to being what we are or assimilate it into this current one,'_ She paused for a moment before asking him a more surprising question. ' _How you feel about becoming a hermaphrodite?'_

' _... Do I even what to ask?'_ Honestly he was starting to wonder if he even had a say in that. Actually, if he did suddenly change genders would he embrace it? He liked it better when he did have the knowledge of what he was thrusted on him.

' _I think it's best that you get some sleep.'_ With that Lucy disappeared retreating back into their soul.

Shinji looked at the clock to his side and let out a sigh. He pulled out the blanket that Misato had gotten for him. It was rather simple with the only unique thing being the image of a snake on it. Pulling it up he closed his eyes and fell asleep.

* * *

Before Shinji, he saw a mirror. Touching the mirror it shattered before revealing himself as a girl. One his own age with the noticeable trait being somewhat bigger breasts for her age. Touching the mirror again it revealed himself yet again this time as he currently was.

It shattered again and revealed himself both reflections one as a boy and as a girl side by side. This then broke apart shattering one last time. Shinji was now back by himself as the shadow covered form of Eva-01 was staring at him. He saw two of himself one a boy and the other a girl standing side by side in front of it.

Before anything else could happen the images morphed into the Angel from before. Shinji took a step back but it was no use. It grabbed him and started to crush him as it pulled him up to its face. Shinji let out a scream of terror before his dream shattered and he found himself on the ground.

A cold wind blew past him as he got up and saw a city. One built in a way that seemed more like a fortress. Two setting suns could be seen in the distance. The plant life was familiar to him yet looking at it he saw several differences to any he knew. "You know it's been two decades since I left this world," Turning his head Shinji saw Lucy looking out at the city before them. She took a seat on a rock as the cold breeze continued past them. "With the way things are going, I figured there wasn't any need for me to stay here."

Shinji turned back to the city noticing what looked like helicopter planes flying out. This was the world that she had landed on before she left looking for Lilith. "What is it called?"

"Sheol," She turned to him as the sky turned red from the sunset. "This world is called Sheol and it is the one that we landed on." The night sky soon appeared as the two moons hung themselves overhead. "You know Shinji all things considered I'm glad that it's you that I was reborn as."

He wondered why she would say that. Before Shinji could get an answer from her the dream suddenly ended as Shinji found himself looking at the ceiling.

* * *

Gendo knew that they would eventually demand that he answer himself. Officially NERV was under supervision by a U.N. committee. Unofficially said committee was made up a group who didn't listen to the U.N. and had throughout history held differing degrees of power over the world. Some of the more noticeable instances in history being the assassination of an Archduke which caused World War One, and the expedition which triggered Second Impact.

Most considered them just a conspiracy theory made up by the fringe lunatics. Those that understood the truth knew they were correct and were afraid of them. They were SEELE and in the post-Second Impact world, they were practically the kings of it. "Tell me why did you demand the Second Child be transferred to NERV headquarters?"

The Commander of NERV looked at the floating obelisks before him. There means of communications with him. A tactic they used in order to appear anonymous. To scare anyone who worked for them. Such a thing was of no use on Gendo. He knew who a few of them really were and finding out the rest was doable given enough time. They knew this and never commented on it nor has he.

"If I recalled your Dead Sea Scrolls do not state when or even if the Second Child was to join the fight," Gendo had managed to catch a brief photo of them. Having read the documents he knew about as much as they did. This combined with knowing half of their names was why they had nothing to target him. "As such, I am within my right as overall Commander of NERV to ask for any resource from the other branches I deem necessary."

Said resource, in this case, was the other vessel for Lilith's soul. Compared to her and the importance of his project the Evangelion Unit was just a tiny bonus. To SEELE it just seemed like he was demanding that they give him another pilot and Evangelion that was already under his command. Gendo watched as they argued amongst themselves. This was a bit of a gamble all things considered. If they didn't allow this then there was a chance that they would look into why he wanted the Second Child.

After several minutes of arguing they had reached a decision. "Very, well you can have your pilot," He held back a smirk at this. "However," The feeling of victory just seemed to disappear. "We will like for you to go on another expedition to the Antarctic."

Soon after Second Impact much of the southern continent became a wasteland. Only the hardiest of lifeforms could survive even the few places were life was still possible. The seas around the continent were only a little better off. SEELE had already sent another group there a few years ago and some of them had died from exposure to the environment. "If I may ask why?"

"During the last expedition a those that returned had confirmed the signs of a fight between the first Angel and another force even stating that there was a Second Spear of Longinus there," SEELE 5 explained though Gendo had long suspected that was the case. Yui had written about it in her notes. Her dreams of the event when Adam first awoke. Of waking up when the giant was defeat and seeing a purple figure which healed her wounds as it was dying. "If you do go and return you are allowed to keep whatever you find as long as you report to us what it is you found."

Gendo knew that a spy would be put in place with them. Still, there were possible benefits to going on this mission and who knows. Perhaps their little spy would meet an accident while on the trip. "Very well."

With that SEELE cut off their transmission as Gendo was left to himself. Walking out of the room he found Kozo standing there. "You know it could be a trap for you."

"I expected nothing less." Gendo adjusted his glasses as he knew to keep a close eye on everyone while he was there.

* * *

When Asuka slept she expected to see the same girl as before. The dreams seemed to always happen on the same day. She was once again standing on the LCL fluid with the giant nailed to a cross. Nothing out of the ordinary and turning her head she was greeted with the girl. She was covered in bandages with only one of her eyes being able to look at her. "Sister."

Asuka's eyes widened in surprise as the girl finally spoke. She called her sister and the strange thing is she felt, no she knew, that this was true. The girl walked up to her and stood just in front of her. "You are Asuka Langley Soryu correct?"

"Yes," Asuka wondered if this was just some kind of reflection of her mind. This was just a dream, right? "Who are you?"

"I am Rei Ayanami," Rei answered as the girl looked at her sister. A strange thing to think about. "I am your half-sister."

This was all just a dream Asuka told herself. She knew that her mother didn't have any other kids. Asuka was an only child. Out the corner of her eyes, she looked at the giant. Never once in her dreams did it move its head. Now it was staring at her and Rei. Her eyes widened as images passed by of her mother and another woman.

Asuka shot up in fright as she took deep breaths. She gripped her head as images flashed. They were brief but it showed her mother asking the woman about how something was made. That _something_ being her. She gripped herself as a horrifying thought crossed her mind. She was made in a lab. ' _B-but that can't be mama would have told me right?'_

Maybe her mother planned to tell her before she went crazy. Before the incident that slowly destroyed her sanity took hold. Asuka shook her head at this. It was only a dream. Those visions meant nothing. ' _I wasn't grown in a lab!'_ Asuka refused to accept that she was just some kind of experiment that her mother made. ' _That was just a dream!'_

Somehow despite her attempts to deny it a small part of her didn't. Asuka pushed that part to the furthered reaches of her mind. Looking at the clock she saw that it was close to time for her to get up anyway.

* * *

Keel stood at his desk as he looked over pictures taken nearly fifteen years ago. On it was a purple giant attacking Adam. At least it seemed like it. The image was so blurry that even with the most advanced image recreation technology could only make vague images. ' _We have an interloper.'_

After everything, he had planned an unknown veritable seemed to have entered into the picture. From the scrolls, he knew that there others besides the Seed of Life and Knowledge that were here on earth. The first trip to Antarctica after Second Impact had confirmed it. Though they didn't find any trace other than a Spear of Longinus which they couldn't reach. ' _Once Gendo retrieves it we can finally confirm if it's like Adam and if it's in a weakened state.'_

He pulled up a report on SEELE secret Evangelion project. The remains of Sachiel were being delivered as he had hoped. From it and the other Angels, they planned to create a special breed of Evangelion. All to be built on the U.N. moon base.

* * *

 **More things change the more they stay the same. So, I think this clears up any questions the last two chapters had while raising more questions. Also, I just used another reference from Jewish teachings because its Evangelion. Yeah, I have no idea what I'm even saying I'm somewhat asleep as is.**

 **Cya all next time!**


	4. Chapter 3

**Must embrace humanity! Yeah, I think I'm a bit hype for Netflix getting Evangelion! We already know this but I just got a Netflix account and I'm having a lot of fun with it.**

 **Thank you** **c0l0r-bl1nd n355, Scattershot98, emotheextremo, and Kaze** **for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Rei stood outside the door to the apartment that was now her home. Her arm was still bandaged up and her eye covered but besides that, she was good enough to be discharged from the infirmary. The Commander had informed her that her stuff had been moved over to this apartment. The door opened up as Misato stopped with a sudden surprise. "Oh, Rei there you are I was almost worried you had gotten lost!" Misato moved out if the way. "Come on into your new home!"

Rei walked in before her eyes fell on Shinji as he walked out. For a moment Rei saw a purple skin humanoid with three eyes and wings. She paused as a name echoed in her mind. ' _Lucifer.'_ Rei blinked as the image disappeared. ' _Where did that come from?'_

* * *

With a groan, Yui awoke to the feeling of LCL fluid on her body. The body of Eva-01 her new existence. Unable to move her body due to it having no S2 organ she had a lot of time to just think to herself. She spent most of the time sleeping dreaming of life. Until the day her son piloted her.

She saw everything in his life. From when her son got abandoned, her husband carting Rei to be used as a means to get him to pilot, and all the emotional trims he was in. If she did have an S2 organ she was going to make her displeasure known to her husband. ' _You promised me and what did you do?!'_

The biggest shock came when she touched his soul. Rather when she touched the soul of both her son and _her_. Lucifer, a Seed of Knowledge like Lilith, the voice that was in her head for close to a year, and the being who nearly died stopping Adam. The only thing she learned in that brief moment was that she had come here for Lilith. Why that was she had no idea except for the one feeling she caught. ' _Did I just give my son two potential girlfriends?'_

Yui, if she could, would have laughed at this turn of events. They were both meant to keep the powers of Lilith out of SEELE's hands. For a moment Yui stopped as she saw Gendo walking out to her pool. If she could she would have reached out and grabbed him. "I know you are angry with me," Anger was such a light emotion. Absolutely furious was more on the level. "And I know if you could I would probably have every bone in my body broken."

' _More like reduced to dust.'_ She had him promise her he would take care of him. Instead, he abandoned their son without a second thought.

Gendo sighed as he took off his glasses. "As I can't make up what I have done I will try to at least make certain that he has everything he needs while the Angels are being fought," Yui if she could, she would have rolled her eyes at this. "When Third Impact is done and you are freed then I accept whatever judgment you have for me."

Yui swore that she did not just hear him say that. She knew the outcome of Third Impact. Of what her father and his friends had planned for humanity. That was the reason she had split Lilith's soul in two. That way either Asuka or Rei would be able to stop it. Except now it seems her idiot of a husband was turning the later into a means to cause it. ' _... Gendo if I ever get out of here I am going to first divorce you and then kill you.'_

First, he breaks a promise and sends their son away. Then he takes over her organization and is trying to ruin her hopes of stopping SEELE. For the love of god what happened to make him this stupid? ' _No worries I can probably salvage this.'_

She needs to talk to Lucifer. Perhaps she would know a way to fix this. All things considered, she really wished she didn't have to rely on her son as a means to save the world. Just shows that even when she tries to be a good person and parent she keeps messing up. ' _At least I'm not trying to become a god and actively tormenting my son for the hell of it.'_

* * *

Rei looked at her new room. She sat on her bed feeling that nothing was broken, unlike her previous bed. The albino girl opened the box that held basically all that she owned. A few books and underwear. There wasn't any need for her to own anything else. A knock on her door caught her attention. "Rei how are you finding your new room?"

Misato entered the room finding the girl sitting on her bed. As far as she or really anyone not in the know knew about her Rei was a strange orphan girl who was placed under the Commander's care because she could pilot an Evangelion. "It's acceptable Captain

"Please just call me Misato," Misato never was one to like the whole captain bit. Rei simply responded with a nod. "Anyway, Shinji's making lunch is there anything you want?"

"Nothing with meat please." One of the few memories of her first incarnation that was edged into her mind was of a failed Evangelion being disposed of. The image was enough to turn her into a vegetarian.

Misato figured that wasn't going to be a problem. She didn't have much in the way of meat anyway. Thinking about it she should probably get some groceries. "Alright then."

As Misato left Rei continued to sit on her bed in silence. The image of before flashed in her mind. The name that brought up and the familiarity. ' _Who is Lucifer and why do I see them in place of Pilot Ikari?'_

She thought about this logically. Perhaps she hadn't seen this Lucifer but Lilith might have. It seemed a bit far-fetched that she was only now experiencing some of Lilith's memories but nothing else made any sense. If that was the case then it could just be that Shinji reminded her soul of Lucifer. "Maybe if I watch him I would understand why that is."

Walking out of her room she found Shinji in the kitchen. To her surprise, she heard him talking to seemingly nothing. "I have a lot of reservations piloting Eva-01 now," There was a pause before he et out a frustrated sigh. "No, because my mother's soul is trapped within it!"

Rei's eyes widened in surprise. He had managed to make contact with her soul after just piloting Eva-01 once? Such a thing seemed next to impossible. Unknown to Rei she was correct in thinking that. ' _Yes, and your mother knew that anyone who tried would lose their soul and body as I warned her.'_

When Misato told him about his synchronization tests with Eva-01 he remembered what Lucy had told him. As much as he wished he could deny it, and oh boy did he wished it didn't happen, on some level he knew it was the truth. How and why he had no idea but now he refused to even get in the ting. ' _Look do you want the Seeds of Life creations to wipe out everyone on this world?'_

"No," Shinji knew that if he didn't pilot that was a possibility. He didn't feel like he had much in the way of a choice. "It's just why did I have to lose my mother for all these years?"

For a moment Shinji found himself within his own soul as Lucy brought him into a hug. His head was pressed against her chest. " _I know but you shouldn't have to close yourself off Shinji I'm always here."_

Shinji found himself back in front of the stove as Lucy's words about her being with him were comforting. Shinji had never really had anyone he could actually talk to about his problems. At least until now with the voice in his head and the woman within his soul.

Rei looked at the Third Child unsure of what to say. Her first thought was to ask how he knew that Yui Ikari was within Eva-01. Another was wondering if she should tell Shinji about his father's plan. If she did it might give him peace of mind and cause him to focus on the objective ahead. ' _I should ask the Commander about this.'_

Shinji finished lunch and turned around almost jumping when he saw Rei. He hadn't heard her sneaking up on him. "Oh, Rei you startled me for a moment."

"I apologize Pilot Ikari."

"Just call me Shinji." He couldn't really take being called Pilot Ikari by her all the time. Shinji had a feeling she would if she didn't tell her otherwise.

* * *

Ritsuko Akagi was one of only three people that knew most of the more classified information of NERV. Among that was the knowledge of Rei true origins. Yui's last work before she became apart of Eva-01. A piece of Lilith in human form. ' _Well, one of them.'_

Gendo had informed her about Asuka. The first hybrid created with Lilith's soul before Rei was a thing. As she was in charge of Rei medical well being the Commander figured it was best that she also take over Asuka's given that she was like Rei. ' _From these reports, Asuka is perfectly healthy though she still hasn't had her period.'_

A genetic quirk of being part, Angel. Rei herself also had it and it was possibly the same for any Nephilim. It was not to say they didn't have the required organs. They did but as for children that was up in question. Even if they could Ritsuko doubted that the Commander would allow it. Rei was given medicine to prevent it while Asuka would likely prescribe it soon after coming to the base. ' _I'm actually wondering how she would take it.'_

The diary of Kyoko was sent to her and had arrived just before Asuka was scheduled to leave on a plane from Berlin to Tokyo-2. When she gets here she would either know the truth of her origins or not. Ritsuko silently hoped that Asuka didn't end up following Gendo's plans. She never told him this but she had read Yui's notes and she knew that if she could his wife would probably beat him for trying to ruin her plan to stop the end of the world.

' _Why is it that I help him then?'_ Ritsuko knew that he was playing into the hand of SEELE. Hell, She suspected that SEELE knew he was hoping to betray them. She wouldn't put it past them. They caused much of the problems for the twentieth century and then had a hand in Second Impact. ' _I'm afraid that's why.'_

Between them both there wasn't anything she could do. The moment she showed disobedience was the moment that she became a liability and a possible target. There was no way out of this as she knew too much. "Senpai the German branch has sent over Asuka's results from her Eva training."

Ritsuko was pulled from her thoughts by Maya walking in. In her hands was files and recordings on disks of the results of Asuka's training as an Eva pilot. Out of the three children, she had spent the longest time training and familiarizing herself with her Evangelion and what it could do. Out of the three of them, she just might be the best in the theoretical side of things. "Thank you, Maya," Ritsuko opened up the file. "Let's see her synchronization rate is at fifty-nine percent the second highest of all our pilots."

She looked over everything else. Asuka seemed to favor close range weapons. Her best with anything ranged was usually with pilots. On that note, Asuka did have a handgun with her that one of the Lieutenants decided to give as her latest birthday present. It explained why she was so good with it. "Randomly entered in a coma after she screamed she was choking at age four and has complained about a phantom pain a week ago."

The first one was around the time that her mother had strangled Rei 1 to death. It seemed that she had felt the extreme trauma of dying that Rei had felt and was sent into a coma because of it. Only coming out of it when Rei 2 awakened. Such a thing was remarkable. Despite being in two different bodies separated by thousands of miles Asuka and Rei could feel when one of the other was in extreme distress. This might be a good or a bad thing.

* * *

Rei sat in front of the TV as she surfed through the channels. She had never really watched television before. Outside of a few documentaries that Ritsuko and the Commander let her see she never really had much in the way of entertainment outside her books. The albino girl stopped as she came across the news. "It had been nearly a week since the attack by a strange monster attacked Tokyo-3," The image of the Angel that attacked the city appeared. Footage of it seemingly shrugging off the JSSDF attacks. "Despite the threat being dealt with by the Paramilitary Organization known as NERV a question of how it came to be has caused many theories to appear."

The theories the news listed was of either aliens, ancient life forms awaken by Second Impact or mutated organism created after Second Impact. The more outlandish called them the forgotten gods of ancient man, the original inhabitants of the earth, or even fallen Angels of God. Watching from the side Shinji heard each of these claims. ' _You know they aren't all wrong in a way,'_ Lucy figured that the full truth would never get out to the public without her or Lilith explaining it. ' _Though I do wonder how long NERV can keep this a secret before links start appearing.'_

Rei changed the channel a few more times before landing on children's programming. It was talking about family members specifically siblings. The door opened up to the apartment as Misato walked in. "Hey, Shinji Rei guess what?" The two of them turned to the woman. "Another pilot being flown in tomorrow the Commander wants you both to greet them."

Rei gave her a nod while Shinji was surprised to know there was another pilot. Why did they call him in if they had another pilot? ' _You know it could be that they are not within the country.'_

Lucy's reasoning made a lot of sense. Shinji wondered just who he or she was. "So what is their name?"

"Asuka Langley Soryu, she's the Second Child and is flying in here from Germany," Misato answered noticing that Rei didn't seem to react to it. She figured the Commander might have told her about it.

' _Talk about coincidence,'_ Lucy had known that Kyoko was working on Evangelions as well. It seemed that like Yui Kyoko had also ended up within one and now her daughter was a pilot. ' _She's the girl that Yui made for her friend and is the other girl that had a piece of Lilith's soul within her.'_

Misato turned her head over to Rei. Asuka was going to stay at the headquarters for a few days. It was to get her familiarized with the Geofront and see the skill set of Asuka before they receive Eva-02 thanks to the U.N. fleet. "Rei listen you're going to have to be sharing your room in a few days time."

"I understand," She really didn't mind that she was going to be sharing her room with her own sister. A part of her was wondering what she would be like. The last dream ended before she could ask her anything.

Misato clapped her hands before turning to Shinji. They were going to need to get things set up and what better person to help them than him. "Ok, Shinji you won't mind helping us fix up the room for Asuka as well?"

"Sure," Who knows maybe the two of them would get along.

* * *

Asuka looked at the pages in the diary not knowing what to feel. It was brought over the day before she was supposed to head to Tokyo-3. As she was the only living relative her mother's diary belonged to her. A page was bookmarked by the folded corner. On that page, she learned that she was in fact lab grown.

She was grown using her mother's DNA and that of an Angel. The DNA of Lilith, a being found within the NERV headquarters in Japan, with her soul bring a part of the entity in question. What's more, it turned out that she was meant to stop Third Impact. ' _D-d-did mama even see me as her daughter?'_

How could she given that she was essentially an Angel? Technically, She was classified as a Nephilim, but that didn't mean anything to Asuka. At the end of the day, she was basically just a vessel and a means to an end. Some part of her climbed desperately to find out if that was the case. The next few entries were about Kyoko thoughts. About what her mother worried for the child and herself. She even worried about what she was going to tell Asuka when she asked about her father.

Finally, after four more pages, she got to the final entry about her leaving and taking her daughter with her. After two years Kyoko had stopped thinking about the fact that her child was effectively the partial reincarnation of an Angel that could doom the world. She was just Asuka to her. The next page didn't have a journal entry but did have a message. "Asuka, if you are reading this then something has happened to me and you now know the truth," There were a few dried wet marks in the paper. "I am sorry you had to read this and you probably think you are nothing more but an experiment or a tool and I won't blame you if you think that."

Asuka read the last lines as tears formed in her face. She closed the book and her eyes. Her mother did love her regardless and never stopped. The image of the girl she saw before filled her mind. She got up with a new resolve. Her mother's friend talked about Lilith being the key to some secret societies desire to cause Third Impact. ' _Like I am going to let that happened!'_

Once she got to Tokyo-3 she was going to find her sister. She was going to defeat the Angels and then she was going to put a stop to the plan to ruin the world. If they don't like it then tough luck! "Don't worry Rei cause big sis is on her way!"

Asuka put the diary into her suitcase as she walked out. She watched as everyone was moving around to get Eva-02 and it's equipment ready for transport. It would take them anywhere from a week to a month to get it all sent depending on if they could use the Suez Canal and if the South China Sea was declared safe. Given that both regions of the world were currently in a conflict that might not be the case.

"Asuka you all set?" She turned over to one of the staff members who was looking at their clipboard. Asuka gave them a nod.

* * *

Shinji blinked as he saw himself looking a tank filled with LCL fluid. Staring at him was a reflection of a woman. In it was a small thing glowing before him. "Yuk I don't know about this I mean," Yui turned her head over as Kyoko looked at the tank. "I mean I am grateful for what you are doing for me, but making a child to house part of the soul of the thing that we been using as a means to create the Evangelions?"

Yui understood what she was getting at. Despite not seemingly being responsive it was very likely Lilith wouldn't take what they are doing to her likely. "I know but if this does work then not only would you have a daughter but we just might be able to prevent Lilith from being used to cause Third Impact," Yui continued to look at the growing form within the fluid. "Have you thought of a name for her?"

Kyoko looked on at the growing creation. This wasn't as she had pictured it but she was having a child anyway. "I was thinking of Asuka."

Neither of them said a word as Shinji continued to watch with them. "You know I am surprised that this memory came up." Next to her was Lucy who crossed her arms. She turned to him with a wink. "Yes, this was from my brief time hiding within your mother's body," The ancient being paused and had a thoughtful look. "Though doesn't that technically make her my mother as well?"

A question for later as the child had already developed into a full baby. Yui began typing away at a keyboard to make sure that nothing was wrong with the child. The new infant opened her eyes for a moment before she was pulled from the fluid.

The next scene was of Kyoko holding a blanket wrapped infant in her arms. Yui looked on as Kyoko held her new child within her arms almost forgetting about her earlier hesitation. While she should feel happy for her Yui couldn't shake the feeling that she had done something wrong. Livy looking at the had a sigh. "Given she had just endangered Kyoko by giving her Asuka she was not wrong."

"Endangered her?" Shinji asked whispering to himself as the scene started to turn dark. The next memory they had was of darkness.

Lucy rubbed the back of her head in embarrassment. This wasn't her proudest moment ever. "So, during this time I thought your mother was suffering an illness and I tried to correct it suppressing the effects until I found the problem," The next scene was Yui holding her newborn child from the perspective of the child. "That was how I ended up becoming your soul."

There were a few moments of silence between them. Shinji stared at her dumbfounded before he finally spoke. "... You didn't know my mother was pregnant?!"

"It was different from the pregnancy I was used too ok!" Seriously, throwing up in the morning mood swings, and weird cravings for food seemed like illogical behavior for a pregnant female of any species. To Lucy, it was almost like some force had it out for them. "I mean I didn't have time to learn how you guys work in depth ok!"

* * *

How long had it been flying in the vacuum of space? About five years all in search of its aunt. Well, not its literal aunt but hey the All-father and her had a close sibling-like relationship so it might as well call her auntie. It started with him lazily flying into the system of his cousins. They made contact with him concerned for their missing progenitor. Seeing how they were friendly and allowed him to constantly pass by and bath in the light of their stars he decided to find her.

As he flew on the intergalactic currents he stopped. The device they have him was picking up radio waves. It looked for any artificial changes in them. At least that was what they had told him. ' _Wait, this region of space is at the edge of the explored galaxy,'_ It was far outside the region of space that the Great Ancestors had planned for their seeding expeditions. ' _Could it be that this is where the missing two ended up?'_

It couldn't hurt to try. They did say that their All-Mother had a talked about finding one of them for reasons. From it's back its Wings of light shot out as it powered its A.T field to full. The solar sail like membranes shot out after the wings as he flew towards the signal. Space warp under the field creating an improvised Alcubierre warp drive. He tapped the device sending a signal to them that he found something.

* * *

 **When not landing on the same world the Seeds can eventually form a degree of peaceful cooperation. Next chapter will have Asuka meet up with the other two pilots. Place your bets how well things are going to go for the three of them given how I have written their relationship as is.**

 **Cya all next time.**


	5. Chapter 4

**So Christmas is coming up soon. Ten days until Christmas. Anyway on with the story.**

 **Thank you knight7572, origamishishou, Scattershot98, emotheextremo, and Kaze for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Asuka looked out at the sun raising overhead as she stood in the train station. Tokyo-3 was before her. As she looked on she stopped noticing her sister standing out amongst the crowd. In a blink, she was gone. For a moment the redhead foreigner wondered if that was just her mind playing tricks on her or if it was a sign that Rei was nearby. ' _If that is the case then I know that I'll run into her eventually.'_

Standing out in front of the train station a group of Section 2 agents walked up to her. She got the description that was given to them by the Commander. "Asuka Langley Soryu," The redhead gave them a nod. One of the agents took note of the red eyes that she had. It almost reminded them of the First Child. "The Commander sent us to take you to the Geofront."

"Well, then let's not waste any time," The sooner she met her fellow pilots and got acquainted with the headquarters the quicker she can find her sister.

* * *

Misato led both Shinji and Rei down the hallways of the headquarters to meet with their German transfer. As they continued down each of the two of them had different feelings about this. Shinji having seen from Lucy the memory of how she came to be wondering what kind of a person she was raised to be.

Rei was for probably the first time in her life excited for something. She was going to see her sister in person. In the back of her mind, she remembered her purpose given to her by the Commander. The scenario required her to get her sister onboard with it.

As they walked into another room the two of them spotted the redhead in question sitting on a chair. Her outfit constated of a yellow sundress and her Eva pilot clips still in her hair. She turned her head as Misato waved at her. Asuka's eyes widened as she saw Rei walking up with her. "Shinji, Rei this is Asuka Langley Soryu, Asuka this is Shinji Ikari the Third Child and Rei..."

"No way you're an Eva pilot as well?!" Misato didn't even get to finish before Asuka raced up to Rei. The two of them stared at one another. As the woman looked in confusion for a few moments.

Rei to the surprise of Misato practically tackled Asuka with a hug. If there was one thing most didn't know about Rei it was that she actually was rather strong physically. If Asuka had been a normal girl she would have been tossed to the ground and somewhat crushed. Asuka instead took a step back before returning the hug. "Can someone tell me what's going on?"

Misato confused expression caused a giggle to echo within Shinji's head. ' _I see someone didn't get the told about their relationship,'_ Taken without any context Shinji mind would have pictured the two of them kissing. In fact, his teenage mind had almost formed the thought. ' _You know I don't mind the thought myself~'_

' _But they are sisters,'_ Nevermind that they also were in some ways the same person as well due to sharing the same soul.

Lucy if she could she would have rubbed the back of her head at this. ' _Well, I admit I am something of a pervert.'_ There was a small nervous laugh from her. ' _Plus I am in love with Lilith you know and there is well two of them together so.'_

Shinji wasn't surprised to hear this. He had long suspected that Lucy was I love with Lilith. It fit all things considered. ' _So you came to earth to confess your feelings to her?'_

' _Actually, I came here so we could continue our relationship and become mates or as you seem to call it getting married,'_ Lucifer answered casually. ' _We both confessed our feelings billions of years ago with the fact we both had to be sent to another world being the only reason we postponed it as long as we did.'_

Shinji had to fight back the shock at this. She and Lilith were hoping to get married. Lucy came all the way to earth in order to finally get practically married. ' _You don't think that they both might of inherited the love for you, me,_ _ **us**_ _?'_

Lucy had a giggle at this as Shinji realized he wasn't really thinking clearly. A slight blush formed on his face at this. As much as she wanted to tease him about this Lucy was actually curious herself. ' _Maybe.'_

Back with the two girls as soon as Rei parted she turned to Misato. She was about to explain when Gendo voice cut in. "It's due to the two of them being long-lost half-siblings Captain."

Misato looked at the two of them. They did have the same color of eyes now that she looked at it and Asuka was a bit pale but not to the extreme of being seen as an albino like Rei. Beyond that, she couldn't see anything that seemed to show that they were related. ' _Maybe they each take more after the parent they don't share?'_

"Captain if you don't mind I want you to take my son out to the range," He looked at the two girls. "I wish to speak with both the First and Second Child in my office."

* * *

Gendo looked as both Asuka and Rei were with him. Before him were the two keys to his plans. The two parts of Lilith. Already though he noticed that Asuka was seeming to take up the role of older and even somewhat protective sibling. Perhaps this could be used as a stepping stone to convince her to go through with Third Impact on a later date. "Now, as you might have figured out," He adjusted his glasses. "I am aware of the origins of both you and your sister."

Asuka froze up for a moment at this. It was brief but she did seem to try to move in front of Rei in a defensive manner. "Relax as you can see I have no I'll well to either of you," He sat back as Asuka calmed down to a degree. "Actually, besides me, only the Sub-Commander and Doctor Akagi know about this."

Come to think about it the diary did say that her mother's friend Yui Ikari was responsible for her creation. She would have certainly known about her. "So only you three and no one else?"

"Yes, the three of us are the only people on this base that know about it," He didn't want to bring up the fact that his wife and very likely Asuka's mother Kyoko, two others who knew the truth, were inside the Evangelions. At least not yet. "Which reminds me seeing how she knows how to treat Rei I am placing you under Doctor Akagi medical care."

To be perfectly honest Asuka never really needed to go to a doctor all her life. She has been surprisingly healthy in that regard. In hindsight, it was likely due to her being part Angel. Though given how her sister was still bandaged up there was still the whole piloting into battle to deal with. "Alright, anything else?"

"Yes, there is the matter of where you would be staying while you are here," Gendo eyes caught a glace to Rei and then back at Asuka. It had already been decided beforehand in order to make it easier for Rei to get Asuka onboard. "For the first few days you would be staying here to help you familiarize yourself with the base then you will be moving in with your sister and my son under Captain Katsuragi care."

Asuka caught the bit about his son being under the same roof as her sister. A part of her mind wondered if he had tried to take advantage of the situation. Knowing how they both looked rather developed for their age it was a possibility. ' _Perhaps I should give him a little warning.'_

What kind of big sister would she be if she didn't beat off anyone looking to take advantage of Rei? If need be she would literally beat them. Asuka was aware that she did have superhuman strength after all.

* * *

Shinji looked as he finally got to see were the Evangelions were kept when not in use. It took some asking but eventually, Misato decided to show him. Both Eva-00 and Eva-01 where kept partly submerged in LCL for reasons likely due to the secret of them being Cyborgs. Shinji silently wondered if his mother knew that he was watching her. ' _Is it possible to get her out of there?'_

Lucy thought about it. On one hand, her body was dissolved practically gone while her soul was absorbed. If the LCL was organic then it would be possible to use it place a basic generic sable to create a clone body and put her soul in it. Though a problem was that the Evangelion would likely refuse to part with it.

On another hand perhaps it was best to remove the inorganic machines and complete the Evangelions growth into a full-on Angel. Yui soul would be effectively reborn in a new body and depending on how they did it she could retain her memories. There was also one other option but that required them to regain themselves. ' _Possibly though if you want her to be extracted from the Eva we are going to need to become whole with ourselves.'_

Becoming whole did mean that Shinji was going to have a gender change. Although Shinji was actually wondering how that was even going to happen. Wasn't their abandoned body back in the Antarctic? ' _Great just have to go to a wasteland.'_ No one ever said it would be easy.

"You know since her here how about we get a synchronization test?" Ritsuko words brought him out of his thoughts. The faux blonde looked at the clipboard in her hand.

Shinji was a bit hesitant to do so. He felt a nonexistent hand on his shoulder. Within his mind, Lucy gave him a comforting smile. Back, in reality, he let out a sigh. "Alright, I guess."

* * *

Yui awoke from her nap as she felt the entry plug enter back into her current form. Was there another Angel attack? No, she was still partly submerged within LCL. As the synchronization rate increased she realized that her son was within it. As the score hit fifty she reached out to him trying to make contact.

To her surprise, his A.T. field shot towards her and in a sudden turn of events, the woman found herself within a dark room. In her confusion, she looked around wondering what had happened before finding her son standing in front of her. "Shinji!"

Shinji looked at his mother. "Mom."

Two purple arms wrapped around him from behind. Yui's eyes widened as she looked at the woman behind her son. Her three eyes stared at her. A smile on her face. "A happy reunion between mother and son."

She finally got to see her. The voice that had been within her head. The person who stopped Second Impact. "Lucifer."

She gave her a wink. As she ruffled Shinji's hair. "That's right I saw you were trying to contact your son and figured I might as well lend you a hand."

Yui walked up to her son as Lucifer moved back from the two of them. Tears formed in the corner of her eyes as she hugged her son. It had been a full decade since she had last seen him. "I'm so sorry I made your father promise me that he would take care of you and it looks like I expected too much from him."

She was so mad both at him and at herself. It was thanks to her that Shinji had abandonment issues. Shinji returned the hug as Lucy watched on. As much as she wanted to let them have the moment there was one pressing matter. "I am sorry to cut this short but it the test appears to be ending."

Both mother and son looked at the ancient entity. Yui looked at her son before giving a sigh. Just went she saw her son again too. "I promise we'll talk later," She hugged her son one last time before looking at Lucy. "Kept him out of trouble if you can alright."

"Don't worry I am always watching out for him," Lucy gave her a wink. Yui was soon by herself back within the Evangelion. If she could Yui would have a small smile.

* * *

Shinji felt rather strange. For one it looked like he was watching out of his own eyes. He tried to move his arm to see if it wasn't something to do with the LCL fluid. Nothing happened as his arm didn't move. ' _What's going on?!"_

Lucy blinked and moved both of Shinji's hands. She blinked a few moments before realizing that she was in control of Shinji's body. ' _I think we might have swap control,'_ Lucy didn't even think this was possible. ' _Don't worry I'm certain we can switch back.'_

That only calmed Shinji down a little bit. Lucy herself looked at her form with a bit of disgust. It wasn't her and yet she was now stuck in it. ' _Hey, I can't help that I am a boy!'_

A few minutes later Lucy in control of Shinji's body walked out of the showers. She looked at the outfit that Shinji had. Lucy wasn't a fan of it. Shinji had a lot of plan clothes with nothing to really stand out. Maybe she could see about getting him something else to wear. "There you are."

Lucy turned her head over to Asuka who was looking at her, or rather Shinji, with her arms crossed. In her vision, Shinji was temporarily replaced with Lucifer and to both of their surprises, Asuka kissed him/her. ' _Wh-what?!'_

Asuka eyes widened before she pulled herself off of them and slammed Shinji/Lucy into the wall. She was confused on why that had happened. "First you are not going to tell anyone that!"

"Sure, sure whatever you say." Lucy blinked as her voice was speaking from Shinji's mouth. Asuka eyes widened as the voice was familiar. The redhead dropped them as she shook her head.

Lucy for her part wondered if Asuka had unknowingly recalled some of Lilith's memories and feelings. It would explain why she randomly kissed them. "Just don't try to take advantage of my sister!"

Asuka walked off as vague images played in her mind. She couldn't see what they were but she could hear two voices talking about being together when they were both finished with their task. "I just got to ignore it and it would go away!"

Lucy watched her as she walked away. She could tell both her and Rei about it. Though there was the problem of having no proof on her claims. Even if she lets it out that she knew about their origins there was kind of the fact that Shinji was claiming that there was another Seed of Knowledge. With a sigh, she whispered to herself. "Well, that is one easy fix gone." She stopped before realizing that she was speaking with her voice instead of Shinji's. ' _I'm going to need to sound like him until we figure out how to change control back.'_

* * *

After finally managing to get the strange thoughts out of her head Asuka figured she might as well see where her sister was currently living. To her relief, Shinji didn't come with her, Misato, and Rei. He said he was going to go for a walk and be home before curfew or something. The only reason Misato let it happen was due to the fact that he would have Section 2 following him just in case something happened.

Asuka looked at the room that her sister lived it. The room that she would share when she moved in. Surprisingly there wasn't much of anything other than a box. "Is this all that you own?"

All she saw was a few books, a broken pair of glasses, and her underwear which happened to be in the box. Rei answered with a nod. Asuka looked at the school uniform that she was wearing. "Please tell me that isn't the only thing you ever wear."

"It is sufficient for all I need it for." Rei answer was not one that Asuka expected to hear. She heard of minimalist but this was just a bit too much.

' _She's doesn't even she much emotion about it.'_ It was like her sister was just devoid of normal human emotions. Even if she wasn't technically human Asuka could say from experience that they had human feelings. "Alright, we are going to go to the mall and get you some actual clothes tomorrow."

Rei wondered why that was important. There wasn't any real reason that she would need any other outfit. Especially given that in the end, she would be dead when her purpose was done with. "I don't see why I would need another outfit."

For a few moments, Asuka wondered if her sister had been mentally abused at some point. She stopped as a memory of her feeling like She was being choked replayed in her mind. ' _Mein Gott!'_ That would explain a lot. For a moment she wondered if she had been abused by her previous caretaker for what she was. ' _When I get my hands on the person who did this!'_

An hour later Misato walked back into the apartment to hear several loud curse words in German. Walking in she saw Asuka looking at her laptop. "Verdammt ihn!" Asuka had looked up the neighborhood that the Commander had made Rei live in. "He placed her in a rundown building!"

Misato had an idea of what she was talking about. She had visited Rei's apartment to get her stuff. The place was completely run down. With the building around it being demolished. Even her apartment was only just barely above falling apart. "I guess Rei told you of where she used to live."

Oh, she did after Asuka managed to get her to talk about her time at NERV. From what Rei told her she had spent her whole life in the Geofront up until a year ago. No school, barely any interaction with other people, and what's more she talked about how she had only gotten a few books to read and the occasional documentary to watch. Rei seemed to think nothing of it. "More than that."

Misato noticed the bitterness on her tone. The nagging question that had been on her mind for a while now came back again. "Hey, so do you and Rei share the same father?"

Asuka was about to point out she didn't have a father. She stopped herself as she remembered the Commander's words. Misato didn't know the origin of her and Rei. "Yes, I just found out two days ago."

Misato wondered what kind of horrible man would leave two different women with a kid and runoff. At the thought of kids, Misato felt a wave of sadness come over her. Her father did manage to save her life, but the effects of what had happened during the ill-fated expedition to Antarctica that triggered Second Impact left its mark. She was sterile unable to have kids of her own. It was kind of a gut punch to know that the option to have kids or not was taken from her.

A bit of drinking would help push those thoughts out of her mind. "Well, you seem to be taking up the role of a big sister between the both of you," Misato paused for a moment. "Truth be told I think it might have a good effect on Rei," Actually having a family member might get her to open up.

The sound of the front door opening up caught their attention. Lucy, in control of Shinji's body, walked in with a few shopping bags in hand. The NERV ID card that they were given could be used as a sort of credit card. On that front, as Lucy found out they did get paid rather well, and to add on they had quit the account already given. ' _I don't know why you decided to get me something else to wear.'_

' _Because everything you have is so simple and I figured you could use something to stand out,'_ Lucy stopped as she saw Asuka who was staring back at her. The thing from just a few hours ago was still fresh on her mind.

Asuka for a moment saw a vision of two objecting hanging over the shy. A purple three-eyed giant and what she felt was her holding hands and making a promise in a language she had no idea how to speak but could still understand. " _It's a promise then when we both get done we'll seek each other out and finally become mates."_

A voice spoke which to Asuka's surprised sounded like it was her who was talking. " _I will miss you Lucifer until then."_

" _I know Lilith."_

Asuka shook her head at this. It was a memory, not one of her own but one of the beings whose soul she had. In her soul, she knew that it was the case. ' _It's just nothing.'_

* * *

Kaworu sighed as he just listened to the music. There was barely anything for him to do and it wasn't like SEELE didn't keep a close eye on him. At least that was what they told him. He suspected they had their attention on something else. ' _I wonder are they planning to find_ _ **her**_ _?'_

He had Adam's soul within him and some of the progenitor's memories. The one that he recalled the most was the last few moments of his life. When another Seed of Knowledge descended from the sky and fought him. The fight did end with Adam's defeat but the injuries he inflicted was likely too much for her and if she didn't die it's likely she retreated into an embryo form as well.

He pulled up his computer and turned off the music. After some tipping, he managed to disable the tracker they put into the thing. Kaworu had long since figured out how to bypass their attempt at keeping tabs on him when he used their systems. Because of this, he was able to access most of their files whenever he wanted. "So the Second Child's gone to Japan ahead of what they expected?"

He tried to access the file on Project Revelation but found that he couldn't. The firewall they had on it was, to put it simply, beyond anything that anyone but they could afford. He was able to look at the planned expedition they had to the Antarctic. "Seems they are going to find her," If they figure out that she is a Seed of Knowledge its very likely they would be planning to use her as a means to cause Third Impact their way. "That's assuming they survive."

Despite being seemingly a lifeless wasteland there was _something_ that was living there. At least the second expedition had said that there was. Kaworu did think that it was possible. While a very, very, very unlike scenario, it could be that much like the Evangelions being born from the flesh of Adam that something akin to an Angel could have been born in the aftermath of the battle between Adam and the other Seed of Knowledge. ' _I could try to warn one of them.'_

As he continued to look through the files he stopped as he noticed something. He didn't know why he had overlooked it the other times he hacked into the system. "What you know I am not tracked like they tried to tell me."

SEELE must have expected him to not learn how to hack into their mainframe. Unfortunately for them being bored with little to do and a computer that plays only so much was just asking for him to get creative. With the illusion gone he wondered what he could do. "You know I think I might go see Mari in person for once."

* * *

 **Well, I been implying that for awhile now that Lilith and Lucifer/Lucy had a deep connection. Oh, and Kaworu now rouge. Then again given he is the Angel of Free Will you can see were that will go. So take your bests on how long Lucy will remain in control of Shinji.**

 **Cya all later.**


	6. Chapter 5

**I'm in a foil mood yet again. If any of you is thinking "I'll write Pokemon" stop your thoughts right there because that place is a war zone. Anyway, trouble aside here is the chapter.**

 **Thank you Dac2003, Scattershot98, and emotheextremo for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

There was one thing both Lucy and Shinji feared. It was going to school. Lucy being the one in control groaned as she learned that she had to wear a uniform. It was strange that there was still school going on even in a city that was basically a war zone no more than two weeks ago.

Lucy stopped when she/he saw Asuka standing outside the school. With the back of the head, Shinji questioned why the redhead was here. ' _Isn't she supposed to be at NERV?'_

Asuka turned her head over and caught sight of both Rei and a Lucy controlled Shinji. She was told that the school was one that both Rei and Shinji went too. Asuka had a bit of controlled fury at the thought of talking to the Commander. After learning how badly Rei was treated by him Asuka had to hold back the desire to choke him to death.

Rei herself looked at Asuka. Her expression didn't change outwardly but much like Shinji/Lucy, she wondered about why her sibling was here. "Have you familiarize yourself with the base?"

"Of course I have," Asuka had a smirk at this. Although as soon as she let it out the Commander thought it was best to enroll her at school. Seeing how Asuka already had a degree it seemed just insulting. ' _I could be a teacher myself but no.'_

Her feelings about this aside it wasn't like it should be a problem for her. Except for the whole fact, she couldn't really read the written Japanese language. She could speak it thanks to her mother teaching her at a young age. Beyond that though she was basically illiterate as for as Japan was concerned. "I'll also be moving in tomorrow with you both."

' _Great.'_ Lucy could hear the sarcasm within Shinji's thoughts at this. After what had happened yesterday he didn't want a complicated situation. Especially with a girl who had conflicting feelings likely brought on by her experiencing the memories of her past life.

* * *

The Angel attack had a surprising impact on the city of Tokyo-3. NERV beforehand had a lot of influence on it before the attack. As to be expected from working closely with the armed forces in what was a fortress city built in both the aftermath of Second Impact and the Impact Wars. Now, the organization was practically in control of the city thanks to the approval of the JSSDF and the U.N. The other impact was that some of the residents of the city had chosen to leave out of a sense of fear.

Some of the school's students had left because of their families moving away. Lucy suspected that come the next Angel attack, and the others that were likely to follow, the student body would decrease to the point that whole classes would start to merge. ' _You know you think they would understand what living in a fortress city means.'_

On her planet, a city like Tokyo-3 wouldn't be that out of place. Tough it would be seen as a bit more relaxed in design the way the city was set up, easy public transportation and road system to prevent traffic, nearby weapons placements in a natural mountainous wall, an underground military base, etc would make it seem to be something of an ideal city. ' _You know I have to ask,_ _ **why**_ _are cities on your world made like that.'_

Shinji for the life of him couldn't understand just what had happened to cause such a thing. He didn't know much about it or it's people even if he did, in a sense. ' _That's probably because of a leftover from a governing structure you call feudalism,'_ Yui was rather knowledgeable in terms of history. It's from her Lucy saw a similarity between the system and the one back on Sheol. ' _It still exists in something on a heavily altered form within my world's current major governing system.'_

The rest of it had to be put on hold as Lucy stopped and looked at the door in front of her. She checked the paper that she was given to make sure that this was the class. "Class 2, yep this is the place."

They walked into the room and saw a few missing desks. Likely from students that were pulled out by their parents moving. Their eyes fell on to a certain ice blue haired albino who was staring out the window. ' _Looks like we got the same class as Rei.'_

The red-haired eye caught sight of Shinji walking in from the reflection on the window. Given the influence NERV had on the school she wasn't surprised by the fact that he was assigned to her classroom. ' _This must mean that my sister will also be assigned the same room as me and Shinji.'_

Rei wasn't the only one to take notice to Shinji/Lucy's entry into the classroom. The whole class started to whisper amongst themselves about this sudden change. Given that, in the last few days, their fellow students seemed to be leaving suddenly having a new one show up caused many to wonder why.

Lucy noticed that one of the students was glaring at them. If she had her powers she could see into his A.T. field and figure out why that was. ' _Maybe he just doesn't like new people?'_ Shinji paused before he decided to make a comment on the whole reading people's minds bit. ' _Also, isn't you know reading their minds an invasion of people's privacy?'_

' _Not really it's how we progenitors, most Seeds of Life based life, and even some Seeds of Knowledge based life communicate,'_ Shinji had to remind himself that Lucy wasn't human. As much as she did understand certain human social cues others were foreign to her.

Lucy took the seat next just behind Rei. Like the albino girl she just chose to look out the window as class started. Given her nature as a progenitor, she really didn't need an education. Each one was basically gifted with extreme intelligence and information so that they could properly establish their colony. Seeds of Knowledge were even given an advance understanding on such things like engineering medical care, and the like for when their progeny develop civilization. Shinji, however, needed an education much to her annoyance.

The teacher walked in as the class took their seats. Lucy barely paid attention to this. The teacher went on that they had gotten two new students. "I see one of them is within the class already you mind coming up here and tell everyone your name?"

Lucy blinked for a moment. ' _Oh, right,'_ Getting up she/he walked to the front. Lucy stared for a moment she tried to recall what to say. She decided to just go with something simple. "Hello, I'm Shinji Ikari please take good care of me." Somehow she made it seem only a tiny bit forced.

Taking their seat the teacher motioned for the other new student to walk in. The door opened as the class started to whisper about the foreign girl who entered into class. Asuka wrote her name on the chalkboard, using the Latin-based alphabet that German used, and turned to the class. "Hello, I'm Asuka Langley Soryu," She noticed Rei sitting within the class and then looked at everyone else. "I'm Rei older sister."

* * *

The whole school was abuzz when Asuka had revealed herself as Rei's sibling. The later had several students ask her if it was true. Rei simply responded that it was true with them being half-siblings. By lunchtime the whole class, possibly most of the school was talking about the sudden turn in events.

Lucy looked on as they watched Rei sitting with Asuka. The redhead looked at the small lunch that her sister had. "That looks far better then what the school is serving did you make that?"

Rei shook her head. She looked out and spied Shinji. "Shinji made it for me."

The albino thought nothing of what she had said. It just seemed like him just giving her food. Asuka, however, felt her protective sister since tingling. Lucy who was watching this could see that Asuka was staring at them. "Hey, Third Child come here!"

Lucy decided they might as well. Taking a seat off to the side. "So, you are cooking lunch for my sister," Asuka had her arms crossed as the memory from yesterday flashed for less than a second through her mind. "Mind me asking why?"

Lucy rolled her eyes at this. Asuka was a bit too much of a protective older sibling. A devious thought crossed her mind. "It's either I cook or Misato does," Lucy actually winced at the taste. Shinji said it best when he complained that it wasn't fit for human consumption. Even if she was as she was as a progenitor, a being who could eat anything organic and even inorganic, Lucy suspected that she wouldn't eat it out of preference. "Besides how bad it is Misato tends to eat take out and I am pretty sure you know how unhealthy that is."

Asuka didn't have a comeback for that. She didn't know if what he said was the truth or not. She looked at the lunch that Rei was eating and then her own. This did not go unnoticed by Lucy. "You know if you want I could make you lunch for tomorrow."

"Really?" It had been a long time since she had a freshly cooked meal. Asuka stopped and looked away. "Not that I would like it," She immediately shot him a glare. "I just don't want to find out you only did this to get with my sister."

' _She's a tsundere.'_ Lucy wasn't that surprised as she did recall that Lilith was a bit like that at first. That and being what people would term a Yandere when she got really possessive. Seeing how Asuka likely inherited that aspect it stood to reason the other one inherited that aspect. ' _... There no way Rei inherited that aspect.'_

* * *

In contrast to her sibling who didn't have much when he moved in Asuka had a lot more in the way of possessions. As Rei looked over them she made note of a doll. It was old and worn. The red buttons for eyes an the threads used for hair seemed to be designed after Asuka herself. Rei pulled the doll up and looked at it. "Careful with that."

Rei looked over as she saw Asuka holding her mother's diary in her hands. "Is this important?"

"Of course it is," Asuka placed the diary on the drawer as she took the doll in her arms. She had a sad expression as she remembered how she had gotten it. "This was the last thing mama gave me."

After an experiment, her mother seemed to have gone mad. She made a doll in her image and for months treated it like her. Until one day in what seemed to have been a brief period of sanity, her mother realized what she had done. She gave the doll to her and whispered an apology. The next day she walked into finding her mother hanging from the ceiling. " _Why mama,'_ A single tear feel out the corner of her eyes at this memory. ' _Why did you have to kill yourself.'_

As she looked at her Rei felt a slight tinge of something. It was like she had lost something important to herself. Something that she couldn't describe. ' _Is this what losing a loved one feels like?'_ Rei knew she and Asuka were connected. Perhaps she was feeling Asuka's sense of loss for her mother. ' _I don't want to feel this feeling.'_

Rei brought her sister into a hug. Asuka was surprised for a moment before returning the hug that her sibling gave her. The redhead whispered into her ear softly. "Thank you."

A small smile formed on Rei's face. The two of them broke the embrace as a knock was heard on the door. "Asuka Rei are you both in there?" Misato voice was heard on the other side of the door before walking in. "Oh, sorry for intruding but it seems that you both are going to have to share the same bed for the time being."

Misato couldn't believe that there wasn't a single store selling them. If that wasn't bad enough it turned out that her delivery got lost in the mail again. ' _Going to have to see why that keeps happening someday.'_

Rei just nodded in understanding. Asuka, however, was a bit worried about this. The redhead had a secret in that she didn't go to bed clothed. A habit that she had picked up when she was younger and one that persisted even when she had gotten several nightgowns. ' _Wait a minute,'_ Rei only had her school outfit and a few pairs of underwear. ' _Does that mean she sleeps in the nude as well?'_

It would make a lot of sense actually. Especially given how little the Commander seemed to care for her. Anger boiled through her mind as she pictured him doing it to a young Rei as something of a sick joke or worse. She had to hold herself back from the rather tempting thought of breaking his face the next time they saw each other. ' _When this stupid war is done I'm taking my sister as far away from that Hurensohn!'_

Asuka pushes out her feelings as she turned to Rei. Her stoic and emotionally underdeveloped sister. At that moment she made a promise that she was going to do whatever she could to make her happy. "Hey, how about tomorrow I take you to the mall to get you something to wear besides just your school uniform."

"Does this have something to do with yesterday?" Rei never did understand why Asuka was so concerned about it. All she needed was to just go to school, to NERV for synchronization tests, and back at her apartment or now back at Misato's. Except for her plugsuit, she didn't have any need to wear anything else.

"Well, yes but that's not only it," She did notice how Rei's uniform did look a bit worn out when compared to everyone else's. She had at least three others and yet it was clear that Rei only ever owned one. It was almost like a certain someone didn't care if she wore anything. "If you have something else to wear your clothes would last longer and already I can tell that your school uniform is worn."

Rei had to admit that her outfit was showing signs of overuse. She didn't care about it given that she wasn't expected to live much longer. Still, perhaps it was for the best if her outfit broke apart then she wouldn't have anything to wear in public. Despite how little Rei put into wearing clothes that at least she knew she couldn't do. "Very well."

* * *

Ritsuko looked at the results of Shinji's synchronization test with Eva-01. It was just amazing how quickly he managed to shot up despite piloting only once before. For much of the test, he had a score within the eighties almost nearing ninety by the time the test ended. All the results from the test seemed to go over well. Except for when she looked over the brain waves scans.

The part about this that surprised her was that both Shinji and Eva-01 had the same brain wave patterns for most of the experiment. Being one of the few who knew the truth about the Evangelions being organic beings they grafted robotic parts on it had been her job to check the Evangelions overall health both during the tests and during deployment. ' _Given the high synchronization rate and the same brain wave patterns…'_

Her eyes widened as she realized what this could mean. Shinji had managed to make contact with the soul of his mother. This should have been impossible without nearing a dangerous level of synchronization. ' _How did this even happen?'_

She went over several scenarios on how this could have been done. The first one that sprang to mind was quickly dismissed. Shinji didn't have any traits of an Angel like Asuka and Rei. Even then the two of them hadn't shown such a thing before. ' _Plus he is genetically related to the Commander and Yui and not Lilith or Adam like the rest of the Evangelions.'_ The second and much more logical answer was that Yui had made contact with her son. ' _If that is the case then what does that mean?'_

Ritsuko made up her mind after thinking about it for a few minutes she decided to tell him about this development. As she walked to his office she saw him talking over the phone. Standing in front of the room she waited for him to finish ad she continued to think about what he was going to do with this development.

The Commander of NERV put down the phone as he finished talking to one of the other branches. The American branch was in a joint effort with the UK finishing up completion with both Eva Units 03, 04, and 05. Given that he had shown he could effectively request any one of them, thanks to him getting both Eva-02 and it's pilot from Germany, there was now incentive to call him about the Evangelion development.

NERV headquarters still had four LCL tanks and Gendo wasn't one to let each Evangelion out of his sight. "Doctor Akagi, what is it?"

Ritsuko handed him the results of the synchronization test with the page on the brain waves being the first one he would see. He had read it in the second that she handed it to him. For a moment he actually had his eyes widened in surprise at what this was implying. Especially when compared to the scans of the brain waves before the test. "Sir, I think Yui has made contact with her son during the test."

* * *

It looked in around its surroundings with confusion. When it awoke it expected the world to be something else then what it found. All around it, life moved. Life that wasn't like it in any way. At first, it tried to contact the strange thinkings that had dug their feet into the ground. Nothing came from it.

They were not like it. On some fundamental level, it knew this. Perhaps the progenitor had failed and one of the others found and colonized the world? These were questions that echoed in its mind. Until it felt a bombardment of information. In its progenitor's dying moments it managed to impart each of its spawn the information on what had happened.

This world should be theirs. Instead, another Seed had landed and took over the world. It had to find it's progenitor and heal it so that it could finish its job. The problem was it didn't have an idea of where to go. After so many millions if not billions of years the land of the planet had changed. Thinking of what to do for several hours it finally realized that it could try homing in on the nearest progenitor signal that it could find. There was no guarantee that it would be its progenitor but at least there was a chance.

It found a signal in a group of islands to the south west of were it had awoken. There it could sense an injured progenitor. This had to be the one for it's kind. Focusing on its power the newly awakened beings A.T. field surrounded itself as it started to float above the ground and towards to its destination.

* * *

Antarctica was once seen as something of a ice filled desert. Even with Second Impact having changed the Earth's axis it was still cold and and while ice no longer covered it salt and even the occasional snow could be seen. What had changed was that few if anything native to the land was left. In a day nearly everything alive on the continent had died out rendering it a true wasteland.

Within this continent, however, something did life. Near what used to be Adam's Seed-ship something began to awaken. A purple handed shot out of the salt-covered ground as a purple humanoid looked around. Its eyes were wild and it's sensing burning. A gaping hole existed within its body. It was missing something important. " _My soul…"_

Its voice was emotionless. The creature looked around trying to feel a signal or anything that would lead it to were it was. A fate pull told it where to go. The missing part of its being was still alive. " _Must unite with it become whole again."_

No matter the cause or no matter how it will take back its soul and become whole. As it walked in the direction ignoring the cold winds and the like something jumped out at it. It was a feral white humanoid about the size of a human. The creature had a hole in its chest and even more, had just a long younger coming out of its mouth. The purple being grabbed it as it roared at her without no care.

This creature was of Adam's remains and it knew that this purple creature was of the thing that killed it. The soulless body of Lucifer tossed the remnant of Adam into the ground. It immediately got back up and faired it's body morphing almost violently shaking as it looked at her with a primal yell.

" _Begone must find my soul."_ The soulless shell said as it turned away from it. The creature didn't take well to this and jumped at it hoping to smash it into the ground. Instead, the soulless form managed to get out of the way and looked for something to pin it down.

Even though it was devoid of its soul it's nature as a progenitor offered it a degree of independent thought without it. It stopped as it saw the Spear of Longinus that Lucifer owned. The object was in a condensed state and while the body couldn't access it in full it still could use it as a means to pin it down. It grabbed the object and threw it into the creature pinning it on both of its sides. " _Stay down I must find my soul."_

It walked away emotionlessly as the creature thrashed uncontrollably under the pain of the spear. Eventually, it did manage to pull itself off of the thing by ripping its body off of it. The pain causing it to roll around unroll it was healed. By then the body of Lucifer was gone.

Said soulless body continued to walk through the cold and contaminated environment without a care. Unfazed by what had happened to the continent the body moved with a single goal in its mind. After a few hours of walking, it found the ocean. It looked at the water before looking straight up. " _I must continue my travels."_

It jumped into the water and as soon as it entered its body began to shift. It's legs mixing together becoming a long tail with a shark-like fin. The water of the earth didn't bother it as it moved through the seas.

* * *

Gendo sat within his office. His mind racing at what to do about the fact that his son had managed to contact his wife during the synchronization test. Somehow Yui and Shinji talked to each other. ' _I have to know…'_ Whatever she told their son, whatever they had said to each other, he had to know. ' _I could order my son to tell me about it and then have him try it again in order to make contact with her.'_

He stopped as he realized that he might have a chance to speak to her. Even if it was indirectly Gendo couldn't waste this chance. Of course, if he just ordered his son to talk to her Yui would tell him about his plan. Even if it wasn't during the second test eventually she will tell him.

This would mean he would have to tell his son about the scenario. It was a necessary evil all things considered. ' _Although how do I keep him quiet about this?'_ He thought about what to do. ' _I'll have to see what he wants.'_

Gendo got up and walked from his office to the Eva cages. Most of NERV's staff were current at home as a skeleton crew walked around the base at night. His mind turned back to the day Yui was taken from him. The day he lost his wife and the day he failed as a father. ' _I know that whatever happens, it will not be pretty,'_ He could picture Eva-01 ripping him in half out of anger as both mother and son take their justified revenge on him. ' _If it comes to that I won't fight back.'_

* * *

 **This is just mostly set up for what is to come next. I know Angels Gambit hasn't been updated and I am already writing it.I might be on temporary hiatus soon. Mostly because I have written nonstop sense january. Had to believe it that I managed to in total make a hundred chapters and only a million words.**

 **Anyway, cya all later.**


	7. Chapter 6

**Another story just before the last five days until Christmas! I almost didn't get to update this today. Way to busy I know.**

 **Thank you Scattershot98, c0l0r-bl1nd n355, and emotheextremo for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Shinji looked around as he saw what appeared to be a moon orbiting a gas giant. The purple color mixed with a dark blue and white creating an almost alluring image. He looked as he saw something land on the moon with him. It was gigantic compared to the landscape. It was brown with a body that was seemingly a snake-like with two large claw-like hands and arms. Its face was seemingly devoid of a mouth. Either that or it was covered in what happened to be a beard. One single eye stared at them. It's sclera blood red with blue iris. The top of its head seemed to mimic a crown as two bird-like things flew around him. In his hands was something that looked like a Spear.

Nothing was said for a few moments before Shinji could feel something spread out from him and touch another invisible thing. A deep baritone voice echoed in his mind speaking a language he didn't know but could still understand. " _I knew I felt a fellow Progenitor somewhere nearby."_

A feminine giggle echoed from Shinji. He heard Lucy speak to this being almost like they were friends. " _I was just passing through and I assume your world is the rather large moon orbiting the other gas giant in this system?"_

" _Indeed it's been coming along nicely,"_ The entity was a progenitor like Lucy and Lilith. Shinji soon realized that this was one of Lucy's memories. " _I forgot to introduce myself, Odyn and I am of the Seeds of Life."_

" _Lucifer, Seed of Knowledge,"_ Lucy answered back to her fellow progenitor.

A hand was placed on Shinji's shoulder as he turned around. He almost jumped before he found Lucy who seemed to be giggling at his actions. "A little jumpy are we?" Lucy looked at the image in front of her with a hint of nostalgia. "You know I had gotten fairly bored at the time when I decided to do a little flying through space before I stumbled on his world about five hundred light years from my own."

Odyn gripped his spear in hand as did Lucy. The two of them then hit each other and they began to push back with each of their strength. Shinji looked on at this a little concerned before Lucy patted his head. "Hey, don't worry this was more his idea for us to have a friendly spare and well given how bored I was I figured why not," The two continued to watch as it was painfully obvious that when it came to fighting that Lucy sucked. "Of course, he won made fun of how bad I was at fighting and then offered to train me how to use my Spear of Longinus as a weapon."

With that said the dream of the memory faded away. Lucy gripped her left shoulder for a moment. She could still remember the pain that he had put her through when it came to it. "It sounds like the two of you had quite the friendship."

"Yeah, though at first I disliked him greatly but after a few million years we became friends," She had a chuckle at an old thought. When one of his creations called her auntie in front of him. "Actually, I managed to find or contact all if the other Seeds by the time I went off to look for Lilith."

* * *

Shinji awoke blinking for a few moments before he realized that he felt like he wasn't just watching his body. Holding his arm up to prove this Shinji found himself back in control of his body. He immediately got up to make sure he wasn't dreaming. "I'm back in control of me."

How this happened Shinji didn't care. He was finally back in control of himself and that was really all that mattered. Looking at the clock he might as well get up and get started on breakfast. When he walked out of his room he stopped as he saw Rei walking out of the bathroom with nothing on. Shinji stopped himself as he shouldn't stare yet his eyes got the better of him. ' _I feel like a horrible person.'_

"Good morning Shinji," Rei didn't even seem phased at all by any of this. In fact, she was more concerned with how he was acting in front of her. "Is there something the matter?"

Shinji just couldn't believe it. She was standing in the nude in front him. He was looking at her body and she wasn't complaining about it at all. ' _I don't see what the problem is either.'_

He couldn't tell if that was Lucy being perverted or if that was just the strangeness of her being an alien. Regardless he felt like a pervert himself and he was doing nothing but looking at her. Misato with a groan walked into the room rubbing her eyes before she stopped and looked at the scene before her. "Shinji, Rei what are you both doing?!"

Rei obvious to the whole fact that she was indecent turned to Misato. "I asked Shinji if he was feeling well when he started to twitch randomly."

Misato just looked at the girl and at Shinji. She didn't know what was more concerning. The fact that Rei was perfectly fine with just standing in the nude, or the fact that Shinji was looking at her. "Rei get some clothes on me and Shinji are going to have a talk."

Rei gave a nod in confirmation. While Shinji stared at his guardian as he felt his spine tingle with fear. Misato crossed her arms in front of her chest as she stared at him. Shinji tried to open his mouth but couldn't form anything. All he felt was shame as Misato looked at him. "You shouldn't have done that you know Shinji," Misato also made note of Rei's actions as well. ' _I might have to have a talk with that girl about her being more careful.'_

* * *

Kaworu walked through the now tempered heat of the Nevada desert. It was in this location nearly seventy years ago that the first nuclear weapons were tested. At the time it was humanities more dangerous weapon ever designed. A title that the Evangelions had been sure to take for themselves. "Fitting really that this is where they decided to set up testing for the three newest Eva Units."

Some part of him wondered how they even made this many Evangelion Units. Sure, Adam was ripped apart by the other Seed of Knowledge and some of his bits were recovered but this many Evangelions seemed like too much for that. Then again they probably cultivated what they had. He stopped as he finally came across the outskirts of the NERV USA base, or as it was once called pre-Impact, Area 51.

"Hey, you!" He turned around and was met with the barrel of an automatic gun curiously of one of the base patrols. Not from NERV itself, no it was from the US Army which held a lot of interest in its branch. "This area is restricted and I am authorized to kill any trespassers leave now."

Kaworu held his hands up at this. Sure he could use his powers to block the bullets but if he did he might run the risk of getting SEELE after him. Instead, he had something to let him get past. "I was sent here by the U.N." He reached into his pilot and pulled out an ID Card one he was able to make thanks to SEELE's rather lax control over him. Q"See."

The soldier looked at in surprised. Apparently, the kid in front of him was selected as a potential Eva Pilot by NERV. "It looks real though I will have to have it verified."

A nod of understanding come from Kaworu. He expected nothing less. An hour later he was walking down the halls of the underground bunkers. Within their cages appeared to be each of the Evangelion that had been built in Nevada. Units 03, 04, and 05. "So Kaworu Nagisa the fifth child," The head of the local NERV branch was looking over his information. Most of which he had faked beforehand except for his name. He just went with the name he was given by the Lilin. "Honestly, with the way, no one tells me anything I won't be surprised if we have a sixth child."

They stopped as he was lead to the cafeteria were a girl around his physical age. "Mari come over here we have someone for you to meet!" The girl in question around still drinking her slushy drink. She finished the last few sips before standing up. "This is Mari Makinami Illustrious the Fourth Child."

' _So this is Mari,'_ Honestly, he didn't have anything to expect in that regard. He didn't know what being half-British even meant. As for the girl in front of him she had glasses over her hazel eyes and brunette hair in twin tails.

"This is Kaworu Nagisa the fifth child." As soon as those words left the base Commanders mouth she looked at him with eyes wide in surprise.

Mari having little to do at the base had tried online chats and from there made something of a front with a guy named Kaworu who also was stuck at some place where he couldn't leave. Now, said friend was standing right here in front of her and was the fifth child. A fellow Eva pilot like her. "No way."

* * *

School was finally over and Shinji couldn't be more grateful. All throughout the class, some guy had been giving him a glare and he was unsettled by that. What did he do that made him so mad? ' _Who knows he could just dislike you on some dumb sense of duty,'_ Lucy had noticed it before but thought literally nothing of it. Shinji did know that one of the students knew about the fight from before. Lucy though deleted the anonymous response that they were given without a care in the world. ' _I mean it's best to just leave him alone chances are he'll leave us alone if we ignore him.'_

The sound of something caught his attention as Shinji pulled out the Angel alerts. To be honest he has almost forgotten that he had them. Asuka who was next to them looked at her own with annoyance. Eva-02 was still out at sea just a day away from making port. She was going to have to sit this one out. Rei was still recovering from her own injuries and Eva-00 still wasn't ready. Lucy was quick to realize that Shinji was going to have to fight yet again on his own. ' _You know hopefully this time it won't end so badly that Yui has to help you.'_

Shinji had a mental sigh at this. On one hand, he knew the weight and the outcome that could happen if he did nothing. On the other hand, piloting the Eva just bought so many problems most of which stemming from the fact that he was kind of piloting his mother. ' _I don't have any choice in the matter.'_

As soon as the three of them got out they saw Misato waiting for them. Inwardly Shinji hoped they didn't have to outrage another N2 mine like last time.

* * *

Gendo looked at the recording feed as the Angel landed before them. The creatures appeared almost crustacean-like as its feelers moved around. Two energy whips moved alongside it as it attacked the nearby buildings. Either looking for something or out of frustration. "What is the status of Eva-01?"

It was the only Evangelion they had on hand that could fight. Naturally with what he had learned Gendo was hesitant to send it out to fight but they didn't have any other options. "Everything is ready for launch sir."

"And my son?" Gendo watched as the Angel moved through the city looking for a way underground.

"The three children are already here the Third Child is being fitted for his plugsuit." With that Gendo stood up from his seat.

The man turned to Kozo for a moment before he walked out of the control room. The Sub-Commander knew that Gendo was going to talk to his son. Strangely enough, this seemed rather sudden given how he normally seemed aloof when it came to him. Whatever the case Kozo felt it was a nice change of pace. ' _Perhaps he is trying to make up for his broken promise to Yui?'_

Unknown to him Gendo was already taken steps for that. However, this time he was going to see his son about his mother. He stopped as he saw him walking out if the locker rooms. There was a moment of hesitation before he called out. "Shinji," His son turned to him as Gendo adjusted his glasses. "You saw her in Eva-01 didn't you?"

He was talking about his mother. For a moment he actually wondered how that was possible. That is until he realized that he was being monitored during the test. Of course, Lucy little stunt would have been found out. "I did."

Words were not spoken between them for a few moments. Each one just stared at the other as the awkward silence filled the room. Shinji turned around figuring it was best to leave. "I-I got an Angel to you know fight."

He stopped as a hand was placed on his shoulder. Turning around he saw that it was his father. Gendo looked at his son before finally finding the words to speak. "When you get back I would like to talk to you about something important for all of our futures."

"Ok." With that Gendo let his son go and turned around to leave. Shinji looked as he walked away as questions formed in his mind. Lucy what do you think is so important that my dad wanted to speak with me.'' _No time for this right now.'_ He had to fight an Angel.

* * *

As the entry plug inserted itself into Eva-01 Yui reached out to her son. As soon as she did she was met with the A.T. field of her son's soul, of Lucy, making contact with her. " _Sorry, but we kind of have an Angel to fight."_

Yui knew that she was aware that they were going to fight. That was why she chose to reach out to her son. " _I know that Lucifer,"_ She could hear the hatches opening up as everything was getting ready for launch. " _I wish to fight with my son so that he doesn't feel alone."_

If two souls were able to see each other in the same way two people could they would see Lucy crossing her arms at the woman in front of her. Then a smile forming on her face at this. " _First, just call me Lucy and second,"_ Lucy surprised Yui by linking her A.T. field with her own allowing her into her son's mind. " _Nice to have you with us mom."_

Shinji within the entry plug heard his mother's voice within his head. ' _Wait, did you just call me mom?'_

A giggle came from Lucy at this. ' _Well, yeah technically Shinji is me after all.'_ Lucy stopped before turning over to Shinji. ' _Oh, Shinji our mother wanted to help us fight outside of you know being within the thing we are piloting.'_

You know if anyone else knew he had voices in his head they would see him as crazy. Shinji was pretty sure on some level he was. Even so, it was nice to know that he wasn't doing this alone.

Within the command center, Maya looked over the reports with wide eyes. According to the readings, Shinji was almost at perfect synchronization with the Evangelion. ' _His sync rate is holding at ninety-eight point six percent!'_

Before she could voice this Eva-01 was already launched rocketing towards the surface and appearing out. Within the entry plug Shinji, Lucy, and Yui all collected themselves as they headed out to face the Angel of Adam.

* * *

The Angel looked on as it noticed the purple giant before it. For a moment it wondered if it was another of its kind. Perhaps it had come to help it find a way to the progenitor. It immediately reached out with its A.T. field in hopes to talk. " _Fellow Adamian are you… wait…"_ It soon saw that it was wearing unnatural skin and armor. This was one of their creations. " _Falsehood!"_

The Angel immediately went on the attack tossing out its whips at the Evangelion. Eva-01 ducked out of the way at this as Shinji looked on at the Angel. ' _That was way to close thanks, Lucy.'_

The Angel smashed into a nearby building a tossed it at them. Yui acting fast brought up the A.T field of their own to block the attack. She heard a comprehensible language yelling at them when she had done so. ' _I have no idea what it is saying.'_

' _It first thought Eva-01 was an Adamian like it, then called us a falsehood, and is now confused when it witnessed us using an A.T. field,'_ Lucy felt Yui 'looking' at her with confusion as to how she understood that. ' _It's speaking the language of the First Ancestral Race it's very likely that it didn't bother with learning any other language.'_

Yui was curious as to what Lucy meant by the First Ancestral Race. She knew there was something missing in this puzzle but she never figured it out. However, She pushed that back for asking her later right now they had an Angel to fight. "Shinji there a weapons cache not far from you see if you can get the Angel busy long enough to get something of use."

No sooner as that was said did the Angel decide to tackle Eva-01. In its mind, it didn't matter that this was possibly some horrifying abomination created from metal and flesh of its kind. It wasn't going to stop him from finding his progenitor. Both it and Eva-01 wrestled one another before one of it's whipped grabbed the cable from behind. " _Is there the source of your power!?"_ Eva-01 pushed him off of itself and with it, the sound of a warning caught Shinji's attention.

Over the speakers, Misato's voice came in a panic. "Shinji the umbilical cord has been removed you only have a limited amount of power remaining!" Shinji looked as a timer turned on showing five minutes remaining.

Inwardly he cursed at this before something strange happened. The timer was not going down at all. "What the?"

This didn't go unnoticed as the scanners within Eva-01 wasn't picking up a power decrease. Instead, something was powering the Eva-01. Ritsuko worked over her thoughts on how this could even be possible. ' _... Could it be?'_

They could never understand why any of the Evangelion could develop an S2 Organ. Even Rei, and possibly Asuka, had such organs even if it seemed to do nothing for them. If Eva-01 did develop one then how and why this had happened? Eva-01 and it's pilot not caring about why they still had power got back up.

The Angel looked at the Evangelion before attacking it again. At this rate, it was starting to wonder what sort of thing the strange creatures had made. "Shinji you have a Progressive Knife in your left shoulder pylon!"

"I know," Shinji reached into and pulled out the Prog-knife. The Angel summoned up its A.T. field as did Eva-01. The two pushed against each other's before Eva-01 was caught within the whips around their neck. The heighten synchronization rate began to show as Shinji felt it difficult to breathe properly.

Even with the Angel attempting to close off his ability to breath Shinji continued forward. He drove the knife into the Angel pushing it through the A.T. field and finally into the Angel's core. The creature let out a large scream before finally dying. Shinji didn't have time to celebrate as he blacked out due to the lack of oxygen.

* * *

As soon as they had gotten Shinji out of the entry plug Gendo wanted a full medical report delivered to him on his desk along with all the scans from when he was in the Eva. Ritsuko furthermore wanted to take a look at the Evangelions organic makeup. The result of which she handed to him in person. "Are you certain?"

Ritsuko gave him a nod as she couldn't believe it either. From the scans, it turned out that Eva-01 was starting to develop an S2 organ. It helped explain why it was able to seemingly not lose power. The keyword being seemingly. From what could be made out the organ wasn't fully developed and could only be relieved on for temporary allowing the Evangelion Unit to move without any power. "I did a double X-ray scan it's indeed there."

This was an unforeseen, if not fortuitous, circumstance that they had. With an S2 organ there Eva Units didn't need to rely on the base power source. Theoretically, it could allow the Eva to better fight the Angels, among other things that Gendo was certain SEELE would make, while fully developing its powers. "Do you think this had anything to do with my son making contact with Yui?"

As for as reasons go that seemed as likely as anything. The only way to prove it was to see about another pilot making contact with the soul within their Eva. The only one that they could think of that might have a chance was Asuka and Eva-02. "If that is the case we won't be able to prove it without telling another one of our pilots about it."

Gendo paused as he thought about what to do about this. There was one thing he knew for sure. They couldn't risk SEELE getting ahold of this information. "Delete your findings from the network…" He stopped as he realized that there was something else they should do. "Also, erase anything pertaining to Asuka and her connection to Lilith."

"Very well," Ritsuko walked out of the room as Gendo wondered if this made things easier for the scenario or if there was actually a possibility that he could alter it. To what end he didn't know.

He looked up at the clock. In one hour he was going to have to make a report to SEELE. Given how intact the Angel, Shamshel was he could see them demanding it to him immediately. ' _Now time for me to just bluff my when talking to them.'_

* * *

Keel stood on the moon base looking on as decades of planning was beginning to come together. The air in the base was thanks to small biodomes each one containing both plants and small farms for grains, fruits and the like. The base power was thanks to both solar and a nuclear reactor. Finally, everyone working here was under numerous official duties in projects that couldn't be traced.

This level of secrecy was so that no one could discover their plans. Keel looked at the first of Project Revelation was growing on the assembly line. The flesh of the Angel that attacked Tokyo-3 was harvested just for this. Soon, the corpse of the next one would join it followed by the ones after that and so on. "It seems that we can't get it to properly develop an S2 organ sir."

The one problem that each attempt at creating an Evangelion Unit, an artificially grown Angel, had always suffered. It was genetically within each Evangelion the potential to grow one. Yet, none of them ever did so. An S2 organ was what was needed for their plans for the project. "Lucky us we have a mostly contacted S2 organ thanks to NERV."

Perhaps they should try an experiment with it. Unit-04 was almost finished in America with a possible pilot selected for the Evangelion. A few actually thanks to a far better understanding of the connection between Eva and pilot and a few modifications that they had made to the system. ' _If it works then we can use the data to figure out how they work and if it fails we still benefit with Gendo losing three new Evangelions.'_

Once they had served their purpose NERV was to be disposed of. It was decided by the rest of the council on what they should do with the organization. Perhaps if Gendo proved himself loyal in the end he would be allowed to join them but Keel won't put it past him to betray them. "Sir, one of the space satellites has picked something flying in our system," Keel turned to one of the workers as they turned in the screen behind him as he watched something flying in from past Neptune. "It's not moving in any way that seems coherent with a comet or the like."

The computer attempted to zoom up as they saw something blurry but it was indeed not like any natural body they had seen. Keel just stared at it as his expression couldn't be seen. "Is there anything else you can pick up from it?"

* * *

It had to slow down as it drew closer and closer to the star system where the signal it picked up seemed to originate from. Now that he was here he makes out that the device he was given was going nuts. This had to be the star system that they were looking for. ' _Judging by the system's size it might take me at must a few weeks to get within the inner system.'_

From there he could check the planets to hopefully find if this was indeed Lilith's colony world. From there he would make contact with the inhabitants and see if his aunt had come to this world. ' _I wonder what did aunt Lilith choose for her creations to look like?'_ He thought about the form that his aunt had chosen for her own ' _Probably something similar to aunt Lucifer's.'_

* * *

 **I think I found this chapter to be something of a challenge. Mostly, because I don't want it to be like the other one. Anyway, Yui fighting with her son/Lucy might become a thing. As for why Eva-02 is developing an S2 organ in this... Well, it's partly due to Lucy being within Shinji when they hit a high synchronization rate. On that note could Asuka and Rei do the same due to housing parts of Lilith's soul? Yes they can.**

 **Oh, and no the thing coming to earth is not a progenitor. That is getting really annoying how many times people say think that.**

 **Cya all next time.**


	8. Chapter 7

**Almost updated this yesterday. Missed out do to me falling asleep. So no three days of updating.**

 **Thank you Scattershot98, and Guest for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

The soulless body of Lucifer continued on regardless of what got in its way. Already the powerful Antarctic currents now brought on by the effect of the Impact tried to cage it around the ruined continent. Yet, the soulless shell did not care in the least and pushed on regardless. The body could sense it's soul and wanted to become whole and nothing was going to deny it this.

As it moved through the water it stopped noticing that there was something within the waves. It looked like something humanoid developing within a crystal-like structure. ' _Seed of Life based Life form.'_

Obviously one of Adams that was close to being hatched. If Lucifer body had its soul it wouldn't hesitate to end it's life before it became fully developed and terrorized Lilith's world. Even without its soul the body still felt an echo of these emotions. Killing it would be logical as to stop a future threat to what remains. However, the pros of Lucifer being whole would render this a non-issue anyway.

With that, the body made a mental note of the creature and continued on. When it reunited with its soul the information would be parted into it and Lucifer could extract the still-developing creature without issue.

* * *

Kaworu looked at the three Evangelion Units before him and Mari. A part of him was kind of horrified by their existence. He was Adam, the thing that they used to make them, and it was like watching someone rip your hand off and then turn it into a weapon to attack you. ' _Does this count as defiling the dead?'_

He turned his head over to Mari who seemed excited for tomorrow. She was going to pilot Eva-04 after they put in a new power source that would allow the Evangelion to operate without needing an umbilical cord. "So, you never told me what's with the look?" He turned over as Mari was in his face. "I mean your hair is it dyed and are those contacts or are they natural?"

"They are natural." He didn't want to add the reason for it due to him being Adam reborn. The whole bit of him being the thing that caused Second Impact would quickly get him attacked by any reasonable human being in the modern age. ' _I wonder why did my past incarnation even do that?'_

He knew that they did start colonizing the world but Kaworu wondered why they ended up on earth. From what little he remembered of Adam's life he knew that four billion years ago the earth wasn't apart of the planned expansion zone. The fact, both him and Lilith landed on the same world meant that they had gotten blown off course. As blown off course as one can in space.

Mari looked at him for a moment. She was looking to see if he was bluffing. "You're serious?"

The two of them heard a few of the staff talking as they passed by. "Hey, did you heard the new power system was just flown in from Tokyo-3 something about it being made after researching the newest Angel."

That caught Kaworu's attention. He was almost certain that it wasn't from some sort of research. They had managed to harvest something from an Angel. ' _Did they manage to get there hands on an S2 organ?'_

The Evangelion Units were not able to develop them. Kaworu actually had one within him. The organ meant that he didn't need to drink or eat. That, of course, was something SEELE loved to remind him. Even though he loved the action anyway. Still, while the benefits of an Evangelion having one would be worth the chance there were several risks that were involved. ' _That might be a problem.'_

"I'm going to go ask about when they can get me fitted for my plugsuit," He gave an excuse and raced the other way.

Half an hour later Kaworu came across the cold storage room. Sneaking into it was going to be just a bit of a hassle. He pulled out his U.N. ID card and hoped that the clearance he had hacked into the system buys it. With a swipe, he waited to see what would happen. The doors opened up as Kaworu walked in. He saw the core that they had within the cold storage held under the blood of the Angel it came from. ' _It looks like it's slightly damaged.'_

The core could be fixed but the S2 organ wasn't properly healed. As soon as the thing was active within Eva-04 the energy within it would expand and rip open a hole within reality, or a Dirac Sea as it was better known. If it didn't kill Mari immediately then being stuck in a pocket dimension with no way out would. ' _Unless I fix the damage.'_

Placing his hands into the fluid he called on his powers. The powers that he had thanks to Adam's soul being within him. His A.T. field touched the S2 organ and simulated its healing process. Slowly the damaged organ regrow and knitted its damage. With his actions done Kaworu removed his hands from the fluid as his A.T. field cleaned the fluid off.

* * *

Mari felt the LCL fluid flood the entry plug as she had a smile. The new power source had been put into Unit-04 and everything was ready for the test of the new power source. Eva-04 synchronization rate began as Eva-04 was brought out into the dried lake bed that would be where they would test it out.

Looking outside as the Evangelion Unit was standing out at the ready. Kaworu stood with the onlookers as the umbilical cord was removed. The operations director speak into his headset from the control room. "Alright, Mari begin activation of the new power core!"

"Finally, I can't wait to see what this can do," With a change the systems within the Evangelion sent a signal through its form as Mari activated the S2 organ. Nothing seemed to happen for a few moments before the sensors within it began to pick up a power spike within the Evangelion.

Everything seemed to be in order. The operations director had a smile at this. "Congrats Mari you're the pilot of the first autonomous Evangelion," The computers began to flash error. "What's going on?"

Kaworu looked up as the Unit-04 let out a roar of pain as the S2 organ within it turned to life. The plates hiding its mouth gave way as the Evangelion Unit began to generate a rather strong A.T. field. Kaworu for his part shot out his own as he tried to calm down the soul within it. To his shock, he wasn't feeling any other soul but Mari's. ' _Unit-04 is soulless?!'_

The Unit then, to everyone watching surprise, ripped off parts of the plates on it as it floated into the air. A white halo forming over its head as it rose into the air. Within her entry plug, Mari began to scream as the LCL fluid within her boiled with a pulse of energy. The Evangelion organic parts began to rip into the specially designed made cybernetic control pieces. A means to allow it to be piloted without a soul. Before finally punching its way into the entry plug. "What's happening…" Mari let out a painful scream as the organic tendrils drilled into her flesh. Her veins bloated under her skin as the tendrils drilled their way into her organs, bones, and finally her brain. "AGHGHHHHHHHHHHHHHHHHHH!"

As she screamed Unit-04 did as well its organic flesh beginning to turn white as wings of light shot out from its back and the ground around it started to rip apart. The computers in the facility blow up one by one as the effect of the A.T. field tore into them. "What's going on!?" One of the technicals was blown back as the computer exploded right in their face.

The Captain turned to everyone looking on from the lake bed. Dust began to expand outwards as the Wings of light from Eva-04 continued to extend. "Everyone evacuate immediately!"

Kaworu looked on as his eyes widened at the sheer insanity of this. They had managed to turn Unit-04 into an Angel. A pseudo-clone of Adam and Mari's soul was being used to complete the transformation. He fell to his knees as he felt her soul scream in pain as it was being forcefully remade by the now born Angel. Kaworu gripped his head as he forced his A.T. fields out clashing with Unit-04's. Out his back, a miniature version of Adams own Wings of Light shot out as he forced his way through the A.T. Field of Unit-04. " _Let,"_ The still being born Angel tried to stop this invasion as it pushed back with all its might. " _My friend,"_ He finally forced his way into the Unit and into the tortured soul and made contact with her broken spirit. " _ **GO!**_ "

The Entry Plug finally ejected itself from the being ripping out a small part of the Near-Angel with it. Unit-04 let out an ear-splitting roar of pain before it was swallowed up by the force of reality ripping apart around itself and disappearing into the Dirac Sea. Kaworu landed on his nears gasping for breath as he sweated profusely. His whole body was in pain at what he had just managed to accomplish.

There wasn't much in the way of time to rest. He got up and ran to the broken entry plug. The organic parts of the Near-Angel breaking apart as he got to it. He gripped the hatch as electricity shot through his body as he grunted in pain. Finally, he got the hatch opened and was greeted with the sight of the white organic flesh within pulsing. After a few seconds, it split open and broke apart leaving Mari.

As the sun broke through Kaworu caught three things. First, she was naked, second her hair was now the same as his and as she opened her eyes weakly they had become a bright purple. None of that was as surprising as the feeling of an A.T field moving past him for a brief moment.

* * *

Gendo sat at his desk as the call came in from NERV's US branch. Unit-04 had been lost thanks to its new power source, the S2 organ they had recovered, causing a sudden change within the Eva before it disappeared. The pilot was recovered though it seemed the result of whatever had happened was not yet revealed to him. "And now your facility is in ruins?"

On the other side, the Commander of the American branches of NERV didn't speak to the Head of NERV. He wasn't wrong as much of the facility was destroyed by the near-Angel attempting to awaken. The repairs would take months but he knew that didn't matter to Gendo. "Yes, but we can rebuild."

"I know but what about your Evangelion Units and your pilot?" Gendo knew he finally had the means to justify holding on to another two Evangelions. After all, it was now time he got the other two before they are destroyed or sabotaged by SEELE. "Perhaps it's best that you place the Units with us for storage while your pilot comes as well for training with our own."

It was a thinly veiled demand for their Units and their pilots. Even if he wasn't told of the fifth child the Commander knew eventually Gendo will demand him. "Fine, I'll see how long it will take to give you what you want."

A smile formed at this. No fighting back at his request. ' _Finally, for once no one challenging my authority in this organization.'_ Gendo was really pissed with how often that happened. He was Supreme Commander, the Head of NERV, and their boss. They shouldn't be trying to question him or fight him whenever he wanted something from them. "Keep me posted on any developments."

Gendo hanged up as he looked over the turn of events. It seemed that merely transplanting an S2 organ into the Evangelions was too much of a risk. At least with Units without a soul. Nearly a whole decade of study had finally accomplished a system were an Evangelion didn't need a soul to properly function. Although it did lose much in the way of performance when compared to one with it, above all being a weaker A.T. field as the ones that the artificial cores they made for the Eva only generated part of it, it was a boon as far as SEELE was concerned.

' _I wonder why they demanded that research be put into developing them?'_ Gendo was suspicious when their Project Covenant, as they had called it, was announced to him. The goal of finding a way to create Evangelions that, according to Kohl's and Ritsuko recounts when reading, wouldn't need souls to function properly. ' _Four Evangelions were planned Units 03, 04, 05, and finally 06.'_

Three of them were completed with one now being lost. Gendo now had two of the Units within his grasp. Call him paranoid but he just knew that the Project Covenant was a test for SEELE. Building on the Project that made the first Evangelions for a purpose he didn't know as of yet.

* * *

Keel was pleased with the results. Sure, Unit-04 had almost turned into a pseudo-Adam, nearly absorbed it's pilot and was lost to a pocket dimension. Yet, in the end, they got what they needed. The data from the S2 organ. The missing piece of the Angels that they couldn't replicate. ' _Until now.'_

With this and the information from Project Covenant, everything was set for Project Revelation. Nothing could stand in the way of their plan. Keel looked at the latest feed from the mysterious visitor. A frown formed on his face as they had managed to pick up a transmission from it. They couldn't translate it but it seemed that whatever it was it wasn't of the earth. ' _It is of no consequence.'_

He got up and looked at the designs for Unit-06. The one Evangelion that had been built with travel to space in mind. It was meant to serve as a means for just in case of this circumstance. Its creation was meant on the off chance that the first expeditions recordings on another creature landing from space to fight Adam were true. "Sir," Keel looked up and one if the base workers came walking in. "Your flight back to earth is ready."

And here he had started to like watching the world from the moon. All good things had to come to an end it seems. "Thank you for informing me."

The worker walked out with a nod as Keel got up from his desk. On the wall, he looked at the recreation of the famous renaissance art of God blessing man. How weird was it that the man with a desire to become God would have such a piece recreated for his desires. As he walked out Keel began to think about Gendo's son.

The Third Child and Pilot of Eva-01. The Evangelion Unit that was made from Lilith instead of Adam. If anything happened it was a backup for their plans. ' _Perhaps I should give the child a reward?'_ Keel was aware of how badly a relationship they had with their father. Perhaps if Gendo turned out to be unhelpful then his son could be used as a means to end him. ' _He is the grandson of one of my associates.'_

A smirk formed on his face at this. Having a pilot in the corner, and one who held such a close connection to Gendo would be just the kind of spy that they needed.

* * *

A blurry white medical ceiling greeted Mari as she opened her eyes. The girl pulled herself back up as she looked for her glasses. Said glasses were handed to her. "Here, I guess you still need these."

She put her glasses on as she saw Kaworu sitting to the side of her bed. "Thanks," Mari looked outside the window as she saw the ground tore apart. A few of the building showed signs of damage. "What happened?"

"That is going to take a lot of explaining," Mari turned to him as Kaworu looked at her. This was rather awkward for him actually. Especially given what Unit-04 had kind of done to her. "So, the first thing the Evangelion Units are not true robots they are actually organic beings covered and made to look like them."

Mari wasn't really all that surprised. She had figured that there was something about them that didn't fit with being a robot. Especially, seeing how they were stored in LCL an organic fluid that was breathable. "I suspected as much," Mari shuttered for a moment as she saw fading scars from were the Evangelion flesh pierced her own. "Is there any reason it went like that?"

Kaworu had several theories actually. "Well, you see each Evangelion is made using the flesh of Adam, the thing that caused Second Impact, and as such, you can say it is a sort of Angel itself."

"... I was basically selected to pilot a brain dead Angel that NERV grew using the thing that caused the world to end up as it did?" When Mari said it out loud it sounded a lot like NERV was trying to fight fire with fire. Although this did make her suspicious on how he knew about this. "So, the power source they put in what was it?"

"An S2 organ that they salvaged from an Angel, it must have caused the Eva to awaken and begin a transformation into an Angel although it was lacking one thing," He looked at her arms seeing the scars. There was another pair on the sides of her neck. Places were the pseudo-Adam tried to consume her body and assimilate her soul. "A soul."

Mari looked at the scars as she placed her hands on them. She had blocked it out but she knew that it was trying to take her. Her soul was what it wanted. ' _I was almost consumed by what was effectively a clone of Adam.'_ She looked at him with an inquisitive expression. "How do you know all of this?"

Kaworu looked away from her as he had a light sigh. He knew that once he told her Mari might try to kill him. Hell, he won't hold it against her to do so. "Because I am actually an Angel, a Nephilim actually, of Adam own flesh," That was only part of it and he knew it. "I'm also the vessel for his salvaged soul," He looked at her as he saw her expression become one of shock. "My Angelic name is Tabris."

Silence fell over them as Mari looked at her friend. Were they even friends? He did come all this way to see her. ' _I mean it could have been to kill me so I wouldn't be around to fight his brethren.'_ If that was the case then she would have been killed by him already. "Why did you come here then?"

"Because the guys who planned for Second Impact to happen were not watching me like they said they were," Kaworu answered as Mari wondered what he was talking about. "Second Impact was not an accident in fact if the expedition hadn't happened Adam would have never awakened, " Kaworu chose to leave out the part about the other Seed of Knowledge showing up for now. Telling Mari about the origins of Adam, Lilith, the Angels, and humanity right now would take to long. "It was done because the committee that oversees NERV are the people who knew about Adam and wanted to cause Second Impact to further their own plans for the Lilin."

Surprisingly enough Mari actually believed him. It would explain quite a bit about the secrecy of the truth of Second Impact, why it was the former continent of ice that Adam showed up on, and why NERV seemed to have cloned Angels to fight Angels. The conspiracy theorists were right after all. "So, you came to see me because I was your only friend?" She paused as she felt like she remembered something. "You… saved me from that thing didn't you?"

"Depends on what you call saving," Kaworu handed her a mirror as Mari took a look at the changes in her hair and eye color. "Your body was partly consumed by it when I managed to get it to let you go with the flesh of Adam assimilating itself into your form."

Mari touched herself as she understood what he was telling her. She was now like him. No longer was she actually human but an Angel. "If that the case does this mean that I am now your sister?"

Technically she did assimilate the flesh and genetic material of Adam into her. While she wasn't born of it did assimilate itself into her being perfectly enough. "If you want to see it like that."

* * *

Asuka looked at her nightgown with a degree of annoyance. The redhead had never really worn it and already she was disliking it. She preferred sleeping in the nude and yet she couldn't do so. ' _Because I have to share my bed with my sister.'_

She had gotten around this by taking Shinji's room for a night but Misato put a stop to that. Truth be told she didn't even want to but having to put this on just didn't feel like her. She'll probably get used to it. Walking out of the bathroom and into the shared room of the two of them she saw Rei having already taken to the bed. Slipping in Asuka closed her eyes and let herself fell asleep.

Asuka blinked as she found herself standing on the LCL covered floor of her special dream. In front of her wasn't Rei but the crucified giant. Asuka walked up as she knew who it was. "Lilith."

Lilith's head moved to her. The progenitor didn't speak to her as Asuka stared at her, at a part of herself. Asuka looked forward as she saw a woman standing in front of her. The lady looked almost like an older mix of her and Rei. This woman had hair that was red like hers but with highlights that were of Rei's. Her eyes had black sclera red iris. From her back was several wings that were white and opaque. Shaped somewhat like that of a Succubi.

Asuka looked at her and then back up noticing that Lilith was missing. Asuka looked back the lady was standing in front of her. "Who are you?"

The lady spoke with a voice that sounded like a harmonized version of her and Rei's. "You know who I am," She placed her hand on Asuka's chest. "I am apart of you as you are of me."

A whisper escaped her mouth as she realized who this was. "Lilith."

"Your sister needs your help ask her about the Human Instrumentality Project," Asuka looked at Lilith wondering what she was getting at. Lilith raised her hand up to stop her. "Whatever you do don't confront Gendo about it when she tells you, try to get Rei to abandon it on her own, and if possible help Lucy to her body."

Asuka looked at her with confusion before her eyes opened up as she found herself awake. Before she could even think about her dream there was something else that caught her attention. She was naked and Rei was cuddling up to her. ' _Wait a minute Rei isn't wearing any clothes.'_

A blush formed on her face as she soon realized that besides that she was also wrapped herself around her. Her heart started to beat rather quickly as she realized the implications that someone would have if they walked in. ' _I should remove my arms off and put my clothes back on.'_

Despite knowing what she should do Asuka found herself not even moving one inch to even do them. Instead, she just laid there looking at her sister slept. Slowly Asuka leaned in closer and closer. ' _This feels so wrong,'_ Her mouth was hovering just in front of Rei's. ' _Yet, it also feels so right.'_

Asuka planted her lips onto Rei's own for a brief moment. The redhead pulled back as she felt extremely dirty with herself. Not only did she just kissed her sister but she had enjoyed it. ' _I am such a horrible person.'_

Asuka tried to move out of her grasp but it seemed that it was pointless. Rei wanted to her to cuddle with and whenever she did the girl used her surprising strength to keep her close. Eventually, she just gave up and found herself drifting off to sleep.

* * *

 **Yeah this chapter was more of one focusing on other people. Also, yeah now Asuka on the path to knowing the truth of what had happened to her sister. Also, I thought of expanding of the development of the Evangelions. If I recalled Eva-01 Eva-02 and Eva-00 (possibly I forget if it was stated) are what could be termed first generation Evas. 03, 04, 05 (and later 06) are second generation with some of the problems worked out. Even if it does come with a draw back but for SEELE it was an experiment that has proven useful.**

 **Cya all later. Happy holidays, and a Merry Christmas.**


	9. Chapter 8

**Two days until Christmas. I have been writing this story a bit more lately. It's not to say I don't write for my others as I am still writing for them. So no worries to anyone who is worried.**

 **Thank you knight7572, and Scattershot98 for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Rei awoke and soon noticed her position with her sister. The two of them close together arms wrapped around the other. Taking a moment to look at her Rei could feel that Asuka was like her also sleeping in the nude. ' _This feels comfy,'_ Was this how siblings normally slept together? Rei didn't know as she never had a family. She was told the reason for why she was born and her purpose in life. That was it she had nothing else. Until it turned out that she did have a family member. ' _I don't want to get up from this spot.'_

As Asuka slept something crossed her mind. A silly little thought that had little consequence to Rei. Moving closer the girl's lips touched Asuka's. The redhead still in a dream-like daze returned Rei's kiss. A blush came over Rei's face at this. ' _I feel… warm.'_

Asuka's eyes opened weakly before they shot open. Her mind was racing at what was happening. She was kissing Rei and Rei was kissing her. ' _Why am I still kissing her?!'_

Finally, after a good second, Rei pulled off of her as the ice blue haired girl stared into her eyes. "Morning." Asuka shot back dragging Rei with her as the two of them fell off the bed. Rei landing on top of her as Asuka felt her leg graze her sensitive area between her legs. "Is something wrong?"

' _We are sisters and we were kissing!'_ Asuka wanted to yell out at her sibling. Those words never left her mouth. Instead, Asuka wanted to forget that this along with what had happened. "It's nothing," The memory of her dream returned to her. "Let's just get ready for school."

* * *

Shinji awoke within a room that he had no idea what it was. All around him was an almost ground like room. At least that was what the appearance looked like. He got up from a cross-like object and raised his purple clawed hand? ' _I'm looking at another of Lucy's memories.'_

Floating to her was the purple colored Spear of Longinus. Her Spear of Longinus having it's colored customized by her preference. It opened itself as Lucy tapped it on the floor letting it excess the Seed-ships scanners. " _No way!"_ Excitement filled her voice as she immediately raced to the opening. Lucy flew out as she looked towards a river valley that the ship was currently passing by. " _They actually did it!"_

She jumped to the valley as her A.T. field moved outwards slowing her down as she floated over primitives fields and farming villages. The start of a civilization. "Wait are they?" Shinji soon saw himself, or rather Lucy, floating down as her size changed growing smaller along with her Spear of Longinus. "Are they all women?"

As soon as she had landed in front of a village Shinji was greeted with what looked like a race of women. The one change between them and the humans of earth seemed to be large wings and a long whip-like tail but otherwise, they didn't seem that different. "Actually, they are a race if hermaphrodites," Shinji turned as he saw Lucy next to him. "I was experimenting with the idea of having several species reproduce like many plants, being both genders, and well, in the end, my sentient turned out to be one of them."

The memory disappeared as Shinji stood with her in front of him. The two of them were then seating across from each other. It was reminiscent of when they first truly met one another. "Shinji I been thinking about it but perhaps I should begin teaching you how to use my abilities."

"Y-you mean I can use them?" Shinji didn't know what she could do but so far what he had seen via glimpses and the fact that she was able to match Adam, the being who caused Second Impact. If he could use that level of power then… He had no idea _what_ he would even do.

Lucy held up her hands to stop him. She could figure what his train of thought was. "First, I did a few years and your current form can only form a minor A.T. defense and feel emotions nothing more," Although Lucy was amazed that they could do even that. "As for my full power, it's very likely that if my body assimilated yours would need time to return to full power."

Even if her body was fully healed she didn't expect it to be able to use her full power. The process of returning to a severely weakened state did mean it had to get used back to using the god-like powers she commanded. "So, I'll just be learning how to use them for when they come back?" That made him look at her confused. "Couldn't you just give me the information due to us being you know the same person?"

"Tried that," Lucy was surprised by how separate the two of them were despite being the same. It was like a wall of will and a sense of self-existence between them preventing them from merging together. "There something blocking that kind of imprint learning."

There went the easy way. Shinji shouldn't be surprised. Even if things did look somewhat up, meeting his mother after so long, his father actually showing something of an interest in him and having someone to talk too, there was always drawbacks. He had expected to wake up and be told he was crippled or something. "How am I going to learn anything?"

Lucy motioned to the world they were in. "I can make a simulation of it while we are here within the subconsciousness," She showed as Shinji felt pushed back by a suddenly appearing barrier. "This way you can learn how to use your abilities instead of having to rely on just practicing while you are awake."

Thinking about that was he asleep? The last thing he remembered while awake was the feeling of something closing on his windpipe. The Angel's wipes crushing on Eva-01's neck and via synchronized pain his own. "Am I unconscious from the Angel attack?"

"Yes, your body is currently resting in the infirmary," Lucy wondered if this was going to become a thing with him. Both the times he fought the Angels of Adam he ended up needing medical care. "We're going to need to get you some combat training as well can't have you always ending up in the infirmary after every battle." She didn't have to tell him twice.

* * *

As soon as he opened his eyes he was greeted to the ceiling of the infirmary. Just as Lucy had said. He wasn't all that familiar with it but still. Shinji turned his head over to the side seeing his SDAT player on the nightstand next to him. It was the one thing his father had given to him if just indirectly.

He looked at the thing as he played one of the tracks. Lucy had once commented about it being rather limited in terms of music. Why an ancient being made with the knowledge and power to shape worlds was complaining about his choice of music was anyone's guess. He sat listening to it for a few minutes before looking at the clock. "Ten thirty-four."

It looked like he had missed school. Given how long he had been out the first time he wondered how many days had past. Getting out of his hostile bed he found his clothes in a bag. A few minutes later after having changed, he walked out of the infirmary. As he walked he was met with Kozo. "I see you're awake," Shinji turned off his SDAT and pulled out his headphones as Kozo took notice of the music player. "Your father wanted to speak with you as soon as you were up."

Shinji figured it was probably about him making contact with his mother. Following the Sub-Commander to his father office, Shinji took note of the rather sparse looking place. The one thing that did catch his eye was the weird graph or was it a tree? Surprisingly enough he felt like he had seen it somewhere before. ' _That looks familiar to me.'_

' _I think it might be something of a symbol used by the First Ancestral Race.'_ Lucy was having trouble recalling where she had seen it herself. Given her vast life occasionally the little things would pass her notice. ' _I think it's supposed to represent a theoretical framework of reality or possibly something to do with us, Progenitors.'_

The last one seemed like an impossibility given there was fourteen of them. Whatever it was Shinji and Lucy could figure it out later. They stopped in front of his father. "I see that you are awake," Gendo turned his head to Kozo. "Thank you for bringing him to me but I would like to talk to my son alone."

As soon as he left Gendo and Shinji just stared at each other. Neither spoke as they looked the other in the eye, or in Shinji's case, in his father's glasses. For a moment there was perfect silence between them. Gendo adjusted his glasses. "You know the truth about the Evangelions I take it?"

Shinji gave him a nod. It seemed he thought that his mother had told him about it. "They are actually organic and are similar to the Angels."

That made things a bit easier for Gendo. He didn't have to explain one of the biggest secrets within NERV to him. "I hope you haven't told or are planning to tell anyone about it."

Truth be told he figured most of the staff had known about it. Although given that he a pilot of one of these things wasn't allowed to know about it did say a lot. "I-I won't," He was going to have to act like had just found out about this instead of being informed via the voice in his hand. "H-how did she end up in it?"

Gendo let out a sigh as the painful memory returned. Shinji it seems forgot all about it. He won't blame him. "She performed the contact experiment, a test to see if it was possible to synchronize with it, and in the experiment, there was an accident and she was claimed by the Eva."

He already knew this. Lucy had warned her the consequences after all. ' _So he abandoned me because of the experiment,'_ He figured that was what happened but looking at his father he could see that the memory stung him. ' _I guess losing mom broke him.'_

"Shinji what I am about to tell you can not leave this room between the two of us," Gendo gaze hardened under his glasses.

* * *

Rei stood with Asuka as the two of them walked into the mall. Her sister had dragged her here in order to get her a much-needed upgrade in her wardrobe. Asuka would have done it a few days ago but the Angel attack had happened and the mall had been closed in the aftermath until now. "Alright, do what your favorite color?"

Rei had no idea what color had to do with her picking out clothes. "I have no preference."

Asuka wasn't surprised by that. She wanted to be but given how her sister was she knew this was likely the case. This did offer them an opportunity to try out and see about what Rei would like. "Let's start with the color blue then."

Her sister didn't respond. She simply gave her a nod in confirmation. A few minutes later it seemed that blue was, if not Rei's favorite color, then the color she most liked to wear as her primary one. Asuka had handed out several dresses for her and each one Rei would try on. Eventually after several visits of a few stores, and a bit of trial and error Rei had with her a few simple dresses and a nightgown. "Here how about a sun hat?"

Rei looked at the thing in front of her before putting it on. She never really had a need to wear something like this. Although her skin was slightly irritated from the sun given her albino skin tone. It was never much of a health issue thanks to her DNA from Lilith but having something to help with it would be nice. "It's acceptable."

After paying for it the two of them walked out as Asuka turned to notice that Rei had opted to wear the sun hat instead of putting it into her bag. For a moment her mind turned to her dream last night. ' _Human Instrumentality Project.'_

Something about it just sounded wrong to her. She had no idea what it was but a feeling deep within her didn't like it. The problem was how she was going to ask Rei about it. About something, she shouldn't know? ' _I could say that I got it from a dream?'_

While at first, this idea seemed stupid. Asuka soon realized that it made a lot of sense actually. If Rei and her did each share a piece of the same soul and they already had shared dreams then, of course, it was possible. As the both of them walked out of the mall to a quiet parking lot Asuka turned to her with a plan in mind. "Hey, Rei last night I had a strange dream," Rei turned her head to her sister as Asuka continued on. "One thing about it that stuck with me was something called the Human Instrumentality Project."

Rei's mind raced on what to do. She wanted to ask how she heard of that. Yet, Her words about it being a strange dream and their connection did open the possibility that it was due to her seeing her own memories. Remembering the Commander's wishes Rei figured that this might be the best time to see about telling her sister.

* * *

' _... Your father is a complete idiot.'_ Shinji could feel heavily restraint on Lucy's part. After hearing his father's plan Shinji did have to agree with her. His father had told him about the Human Instrumentality Project.

He explained that it was a plan to return humanity to a more simple existence while merging their souls in a way to have each one strength dissolve each one's weaknesses. Gendo was planning to use the project as a means to free Yui from her prison within Eva-01 and reunite her with them. Just hearing this made Lucy wonder how criminally insane was these idiots were. The Progenitor knew that such a thing wouldn't make humanity whole nor would it removed their flaws.

The merged thing would be nothing but a zero-sum. Each of the strengths and the weaknesses would cancel each other out. In the end, the actions would only create a crazy barely recognized remnant of humanity. What also enraged her was the fact there was only one being who could have done this. The being she loved, Lilith. ' _Oh, and never mind what such a thing would do to us!'_

Unlike humanity who would be driven into a nimble near blink state both Lucy and Shinji would be able to remain separate. That is if the power of their soul didn't drive humanity into a permanent state of insanity while they are forced to be stuck on a barrier would in a sea of primordial soup. If they manage to get back Lucy body and assimilate it or return to it then they would be the only living thing on a dead wasteland of organic sludge. Admittedly in that scenario, there was a chance that they could undo the damage but depending on how hard and long it took at best they would only be able to save a fraction of what was.

While Lucy was mad at learning at the idiocy of this plan. Shinji was highly concerned about what it meant not only for humanity but for Rei and Asuka. "S-so, you th-think that this is the only way to get her back?"

Gendo answered with a nod. For his part, Shinji managed to block out the numerous curses that Lucy was yelling right now. Some of which likely came from her world. "Yes, I do."

' _Shinji,'_ Lucy's voice was calm. A sort of calm that would unnerve anyone. ' _We are going to tell Asuka about this.'_

That caught Shinji's attention. It just seemed rather sudden that Lucy wanted him to tell the redhead about all of this. ' _Why Asuka?'_

Lucy, if she could, would be glaring at Gendo. The ancient being just knew what he had done. ' _Shinji, only Lilith can perform this Instrumentality and I know for a fact that she wouldn't go for it,'_ Shinji wasn't liking where this was going. ' _However, Lilith now has two other personalities connected to her in a similar fashion to us and while one of them is well adjusted and understanding of humanity, the other one has most likely been mentally conditioned by your father.'_

Now he understood what Lucy was getting at. Rei was a piece of Lilith's soul. If she returned to Lilith then there was the possibility that she would take control and do what Gendo wanted. Asuka being the other piece of Lilith was the best chance they had at preventing that from happening. Still, the fact that Gendo had effectively been treating Rei like a tool was kissing him off. Especially, given he was likely going to try it on Asuka as well. ' _I never knew I could hate my father even more than I do now.'_

Gendo pulled out a NERV ID card that had his name on it. On it was his new rank as a Flight Lieutenant. Making Shinji effectively the highest rank Eva pilot. "Besides you and me only Doctor Akagi, and our Sub-Commander know about this," He handed him the card. "Do not talk to anyone but them about it."

"Yes father," Shinji answered as he pocketed the card. He knew that his father was likely omitting a large part of what was actually going on. Lucy pointed out part of it that his plan needed Rei and Asuka. ' _Lucy, who do you think would want to do such a thing like Instrumentality to the world?'_

The idea of some secret society popped into Lucy's mind. She had seen several such things happen before. Groups working from behind the scenes in order to control anything from cities to whole nations. It would make sense that one could have found clues either after Second Impact or perhaps even before it. Thinking about it the later seemed a bit terrifying.

* * *

Asuka couldn't believe it. Rei had told her a brief summary of what Human Instrumentality was. The returning of Lilithian life back to a primordial state. The merging of souls so that the strengths of each would remove their weaknesses. As soon as she had finished Asuka felt the urge to yell about how crazy it sounded. For some reason, Asuka felt that this wouldn't happen as Rei had explained it.

She kept quiet as Rei explained that it was her reason to be alive. A little voice within her head, a feeling that Asuka had within her, told the redhead that this was a lie. Only now that they were back in the apartment did she understand why Lilith had appeared in her dreams. This whole plan had to be the Third Impact that her mother's friend was talking about. The plan to use Lilith to permanently change the world. ' _And my sister is being conditioned to accept it as her purpose?'_

That didn't sit well one bit with the redhead. Rei shouldn't be treated as a mere tool. She was ok with the possibility of dying when all this was done. She clenched his fists as her mind turned to Gendo as rage boiled within her. "It's all his doing that bastard!"

"Who's doing?" She turned around to see Shinji. The son of the man she was currently angry at.

Shinji flinched under her gaze as her sclera seemed to turn black when she looked at him. "Your father," Asuka narrowed her eyes as she walked up to him. "Tell me do you know what your dad has planned for my little sister and me?"

Inwardly Shinji wondered if she was talking about Human Instrumentality. On one hand that did make this easier for him. On the other, the look she was giving him was terrifying. _Shinji you were going to have to tell her anyway.'_

While Lucy was true that he did come to tell her about it. Although looking at her glare made him want to rethink this plan. Feeling a nonexistent pat on the back from Lucy he figured he might as well do it now instead of later. That might just piss her off more. "Y-you m-mean Instrumentality," Asuka's gaze hardened as Shinji held his arms up at this. "Wait my dad only told me about it because I managed to contact my mother's soul with Eva-01," He started to panic at the end a bit. "His plan completely insane!"

Asuka paused as her anger give way to a questioning look. Did he just say that Eva-01, the giant robot that he piloted, had his mother's soul? ' _Why would he say that about a giant robot…'_ Her mind put it together after a few moments. Robots didn't need to be put inside an organic fluid when in storage. They also didn't need to have certain people be able to pilot it. Furthermore, a robot shouldn't be able to replicate some of the things an Angel could do organically. ' _But if it's not a complete robot.'_

Her eyes widened before she realized her mother was talking about the problems of growing the Evangelions. It made a terrifying amount of sense. The reason the Evangelions could fight and win against the Angels was that they were made from Angels themselves. "You're mother's soul is in Eva-01?" Asuka froze up as the implication that this created cross her mind. Why she had been chosen to pilot Eva-02. ' _Gott, bitte sag es mir nicht.'_

Was that why her mother was so broken? Did that mean that Eva-02 housed her soul? Asuka shook her head pushing these thoughts out of her mind. She had to focus as the two of them had a lot to talk about. The revelation of the Evangelions being partly organic could wait. "You and me have a lot to talk about."

* * *

Yui was again bored out of her mind. Being locked within the body of an Evangelion with no way to move or do really anything, Yui had grown used to the feeling. Her first thought was to take a nap and sleep until a synchronization test. At least until she discovered something weird by accident.

She could project a weak A.T. field. Likely thanks in part to the S2 organ powering the Eva. Remembering how Lucy had used their A.T. field Yui tried to replicate the feat. She failed several times when trying to talk to Eva-00. At least that's what she thought. ' _Maybe I am just doing something incorrectly?'_

She almost wondered if she could use her A.T. field to talk to anyone. Yui knew that the Evangelion to the left of her was Eva-02. She had seen its pilot when they brought Eva-01 back to base. The girl that she made for her friend. ' _Kyoko,'_ She did say that she was going to complete the first of the production models. A finalized creation intended to be used as the bases for Evangelions going forward. ' _I'm sorry that this all happened to you and Asuka.'_

As she continued to wonder what her old friend was thinking Gendo walked into the room. For a moment Yui debated if she should move her arm and crush him in her hand. With the S2 organ and a lot of concentration, it was possible for her to move her arm reach out at him. That is if she wasn't heavily restrained. ' _I know the precaution is due to the S2 organ that Eva-01 is developing, but I can't help but feel like you did this so I can't crush you.'_

Gendo looked on at the Evangelion. He was certain that his wife, well legally still his wife even though Yui wanted to not even think of herself as such, had taken notice of his appearance. "I told our son about my plan to save you," That and give him command over his fellow pilots. "He seems to be onboard with it."

' _I highly doubt that,'_ Yui was certain that Lucy had already told him how stupid it was. It's more likely he was just faking it.

The Supreme Commander of NERV turned his attention over to Eva-02. He had occasionally been told by what little reports that the first production model as it was called would be perfect for the upcoming war. Yet, he knew it was just boasting done by the German branch. They had no intention of bringing it here until he basically took it. ' _Perhaps I can see if there was some truth to Kyoko's words.'_

* * *

 **You know even when Gendo is still somewhat not a total asshole I can't help but make things worse for him. Is that mean of me? Right, of course, not. I chose to not write an explanation from both Rei and Gendo on Instrumentality because you all very likely know what it is already and plus it would be repetitive. Speaking of which SEELE is not foolish enough to use one or two routes in their plan. I mean they now have three more ways to do it. If you can guess all three (excluding using Eva-01) then I'll give a shout oout to you next chapter.**

 **Cya all next time.**


	10. Chapter 9

**Marry Christmas everyone.**

 **Thank you Scattershot98 for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Asuka stared at him as Shinji finished telling her about how he came to know of his father's plans. After hearing it he decided to come to her as He suspected that his dad needed both her and Rei to complete it. He did leave out the fact that Lucy was the one to tell him to talk to her, or that Lucy had informed him of their heritage. Instead, he explained that his mother told him about both of their origins.

Surprisingly she felt herself trust him that he didn't agree with this. She looked at the card he was given from his father with her right eye twitching in annoyance. ' _He bribes his son with a higher position after he tells him everything,'_ That was rather low and the literal definition of nepotism. "He makes you a Flight Lieutenant just because he tells you this?"

"I have no idea what it means actually." Shinji's military understanding was rather poor. In fact, outside of a few commonly known ranks and the basic understanding of the military, he knew literally nothing else. "I am guessing its something important?"

He was given a nod in confirmation by the German girl. She hated it so much but right now hatred for his father was almost natural. "He just made you both mine and Rei's superior in terms of rank."

In the back of his mind, Shinji could hear a mocking laugh from Lucy. She knew what this was. An attempt to kept them quite. ' _He thinks it's sweet of him?'_ Shinji found himself staring at her within the realm of there soul. Her arms were crossed in anger. "He a fool who has lost his mate and is taking it out on everyone else including us," It almost looked like to him that fire seemed to burn off of her body, though it could have just been her projecting her anger. "Son of a bitch!"

"Would you have done the same for Lilith?" Shinji had a feeling that some of her hate wasn't just directed at Gendo for his plan. Some of it was directed at herself.

Silence filled the soulscape as Shinji continued to stare at her. Lucy looked away from him. The thing she hated most about all of this was how correct his thoughts were. "Lilith would never ask me to do something like this, by the pit, she had to make me promise to build my own world," There was a small blush of embarrassment at this. With human context, it was like she was a clingy girlfriend or a silly little girl who wanted to follow her crush around. "But if she did…" Lucy turned to him with an emotionless expression on her face. "Then I would even if I didn't agree with it."

As soon as she said that did the little soul talk ceased as Shinji was brought back to hear Asuka. ".. going to get my sister to abandon it and you are going to help me!"

Shinji blinked for a moment as he wondered what did he just miss. He looked as she looked at him with a stern and determined look in her eyes. Even though he had just been effectively roped into her plan, whatever it was because he only got the end of it, Shinji didn't seem all that bothered. ' _I guess something like that would be passed on to me.'_

* * *

Ritsuko looked at Kozo as she was amazed by what she had just heard. Gendo had told his son about Instrumentality. Now, besides them and Rei he knew about it. 'What she couldn't believe was why Gendo would tell his son about there being a secret Cabal that existed who basically Run much of the world. ' _Assuming he even told him about it.'_

Knowing him, of course, he didn't tell Shinji about SEELE. Why tell your son about the organization that been manipulating nations for about a hundred years. More if Gendo was to be believed. "Does he even know how that will come to be?"

Kozo shook his head at this. Ritsuko wasn't surprised in the least to see him do this. "It didn't come up but if he does ask I believe that he would be allowed to know that answer."

' _Yeah, know that both Asuka and Rei are going to be returned to Lilith to cause the Impact.'_ Seeing the redhead girl and how independent and alive she acted when compared to Rei caused her a great deal of shame. These were two girls that both held a piece of Lilith within them. In a way, Asuka showed her what Rei could have been. A relatively normal girl.

This was when Ritsuko realized how danmed she truly was. Not only was she helping end the human race, taking part in an organization that made child soldiers, but she had aided in the mental abuse of a child. The worse thing is even if she did manage to not get killed while revealing everything then what would happen then? There was no way she could live with herself. Killing herself wouldn't work in any case. She was certain Gendo had a plan for just that possibility as well.

"Also, there was an incident with the activation of Unit-04," That wasn't exactly unexpected to hear. They were forced to hand over the Angel's core without seeing if the attack add damaged the S2 organ. She expected it to do anything from exploding to maybe even rip a hole in reality. "The pilot has survived but the base in Nevada is now broken."

Didn't take her long to know what this meant. They still had spare LCL tanks for the Evangelion Units. Eva-03 and Eva-05 were being built in America and should already be finished. "He's taking both their Eva's and the pilot isn't he?"

* * *

Mari stood put in the temperate desert as she began practicing her new abilities under Kaworu watchful eye. After he told her the truth of everything about him and what had happened he figured it was best he taught her how to use her own abilities. ' _She seems way to accepting of this.'_

The girl had quickly adapted to her new state of being extremely fast. There was no angst over being a member of the enemy. No horror on the knowledge that she was now a Child of Adam. Even when he explained that her soul had been remade into one of a Seed of Life she just seemed to accept the change. Mari even went so far as to try to give herself an Angel name. "How do I do that thing that lets you, you know float in the air?"

"That's due to our A.T. field and at how you are I don't think that would be a good idea," Plus there was the fact that SEELE and NERV had tracking satellites in orbit that could pick up on A.T. field bursts from space. The reason being because of First Impact.

That was another thing he had told Mari about. While he didn't remember it from among Adam's memories he did put it together when SEELE talked about the Dead Sea Scrolls talking of Angels from space. Adam's Seed-ship ended up on Earth first and before the first of his creations could properly receive their souls Lilith's crashed into the world. The moon was made from the debris tossed in the aftermath of the Impact.

Some of the still then infantile Angels were now developing in the moon or on asteroids floating about the solar system from the collision. Seeing how it would help to locate them SEELE had sensors put in place and space telescopes that would track them. The thing was they did still pick up earth based A.T. fields, if extremely faintly.

Beyond that Mari still had some trouble properly summoning her A.T. field. A consequence of being born human or Lilin as he told her. Apparently, it was what the Black and White Moons called the race that had formed from Lilith's genes. "Right, still haven't formed my wings for the first time yet."

"You know I been meaning to ask why are you so unaffected by the whole change," Mari looked at him with a confused look as he got off the rock he was using as a bench. The clouds overhead blocked out the sun as things turned temporary dark.

Mari shrugged her shoulders. Sure in an instant everything about her was no more. It was all do to a test of a salvaged S2 organ turning the Evangelion Unit she was piloting into a clone of Adam. "Well, yeah I guess I should be but really this just created so many opportunities," Kaworu couldn't understand why she was so chipper about this but maybe that was just because he didn't know what she was thinking. "Say, you didn't tell me is there any other changes besides just the ones I can see?"

"I could scan your body if you want," He wasn't well versed in Lilin social norms. If he did he would have realized what he had just said.

A giggle escaped Mari's lips at this. "Why Kaworu you like what you see?" Kaworu looked at her for a moment before he started to put two and two together. A blush formed on Kaworu's face. "I'm only teasing you," She had a curious look on her face. "Although how will you do it exactly?"

Kaworu pushed away this awkward moment from his mind. He might have to watch what he says next time. "I'll use my A.T. field to do it," It was an ability that he had thanks to being the reincarnation of a Progenitor. "It won't let me actually see it but it would give me an idea nonetheless."

Mari gave him a nod as Kaworu's A.T. field entered her. Her own A.T. field acted on instinct. Yet, surprisingly instead of resisting him, it seemed to welcome him. Moving his A.T. field through her body he saw that like him she had an S2 organ much as he did. Her organ structure while appearing like that of a Lilin had the marks of being a Nephilim. ' _What's this?'_ The biggest change was in the part of her body that served the role of reproduction. ' _She… she has the ability to give birth to Angels.'_

He wasn't just talking about beings like them. She could do that too. Instead, he was talking about giving birth to Adamian Angels. ' _Is this because of her being nearly assimilated by the ascending Evangelion?'_ It was made from Adam's flesh. If it didn't suffer much in the way of genetic mutations from creation that it was possible that she would inherit some of Adam's progenitor nature. ' _I have to tell her.'_

His A.T. field retreated from her as Mari seemed to shutter. She didn't expect this feeling to come about from it. "So, what is it I don't happen to have two hearts and the ability to turn into different versions of myself at near death?"

Kaworu didn't get the reference. As for as he knew she was being serious. "Nothing like that," He shook his head. "You do have an S2 organ which is active although the thing that might be concerning is that you have the ability to well make Angels," He pointed to around the part of her body where her womb was. "The things there are able to produce Life Cores, the bases for Adamian life, Angels as the Lilin call them."

Mari's hand moved over to her stomach. There was something of an emotional blank as this set into her mind. She had the ability to give birth to Angels. "I have no idea how to feel about that."

* * *

Rei stood out on the floor of LCL. Nothing was around her as she walked on the fluid. Strangely enough, she expected to see her sister or maybe Lilith. After no change happened to her Rei was about to turn around and see it was possible to wake up. Instead, she was greeted with a copy of herself standing hunched over. Before she knew it the copies arms reached out and grabbed her neck.

"Why?" The copy spoke to her as it applied pressure on her neck. It raised its head as Rei stared as her copy bleed from the holes where her eyes should be. "You care nothing for your duty so you throw it away?!"

Reaching out of the LCL was numerous broken bleeding bodies of humanity. They each stared to her as Rei stared back an unknown feeling on her face. The feeling of fear. They all spoke in an almost demonic chorus. "You'll doom us all to an endless hell!"

Finally, behind them, she saw her sister. Asuka crucified on the same cross as Lilith. Blood coming out of her wounds her chest implied with a spear and one of her eyes missing. Despite the apparent corpse like nature of her body Asuka still turned to her. Her last remaining eye glazed over like a corpse. "This is our fate if you continue down the path you been following."

Before she knew it the broke remains of humanity grabbed at her as Rei was forced on to a similar cross. Pain shot through her ad the hammered two nails into the palm of her hands and into both of her feet. Razor whips latched out at her as tearing deep gashes into her body. The cross was put up as the pain-ridden Rei could see Asuka in front if her.

Out the corner of her eyes, she saw the broken body of Lilith this time ripped apart as LCL fluid just flowed out of her. From her eyes, tears of actual human blood poured from them. "Behold the greatest betrayal of humanity!"

Rei looked as she saw Gendo missing an arm bleeding out from an untold amount of cuts hold a spear in his hand. A wicked and sadistic grin was on his face. "Thank you for helping me!" He thrusters the spear into her gut.

A gasp was heard as Rei awoke causing Asuka to wake as well. Seeing her sister in a panic Asuka was immediately filled with worry. "What's wrong?"

After a few more breaths the albino girl got a hold of herself. This was just a dream nothing more. Her sister wasn't crucified on a cross and humanity were not trying to crucify her. "It's nothing."

Asuka looked at her as she didn't' believe it. With the sudden awakening done Asuka realized that both her and Rei were naked again. Despite both of them having put on their nightgowns beforehand they had both removed it in their sleep and returned to cuddling each other. ' _Why is this happening?'_

* * *

Misato walked into NERV headquarters as she watched the three Evangelion Units they had being set up in the cages. She saw Ritsuko talking to the Commander looking on in disbelief. "Having both Eva-01 and Eva-02 on hand for when we try to get Rei to synchronize with Eva-00 I understand," Her expression now that Misato noticed it was of disbelief. "But wanting both the Third and Second Child to do a Coss Synchronization Test between their Evangelions?"

Gendo adjusted his glasses at this. "We already know that Rei can pilot Eva-01 if a need arises but what about my son or the Second Child?"

Both he and Ritsuko knew that it was theoretically possible for Asuka to pilot Eva-01. Being part Lilith herself her much like Rei such a thing was possible. Ritsuko knew he was just needing an excuse to test the theory. "Fine."

With that Gendo left as Ritsuko wanted to rub her head in annoyance. It was going to be such a hassle to reconfigure both of them. Add on she didn't know much on the programming for Eva-02 because, of course, the German branch forgot to give it to her. "Sometimes I think he just orders things to make everyone miserable."

"What's this about a Cross Synchronization Test?" Ritsuko turned around to Misato.

Given her role of Operations Director Misato should have known about it. Although given it wasn't an issue when they only had one pilot it might have been that Gendo didn't think she needed to know. Wouldn't be the first time actually. "It's in case something happens to one of the pilots while we have an Eva down," Ritsuko eyes turned to Eva-00 as she said that. "The test is so that we know which pilot can serve as a substitute for each Evangelion."

Misato knew that the minimum synchronization rate needed for one to be able to pilot an Eva was twenty. Anything below this would end with the Evangelion barely being able to move. She should know she did try to have actual pilots attempt it and none of them got past one percent.

* * *

The three children walked through NERV with Misato leading them. As soon as school was over with she had come to get them. Rei was to have the last of her bandages taken off and a test with Eva-00 again. "Wait you mean to tell me she was injured because of a failed synchronization test her Eva?!"

Maybe telling Asuka about the last time wasn't such a good idea. Hearing how the last test with Eva-00 injured her little sister made Asuka mad. The redhead was starting to wonder if they were just going to keep doing it until she died. Misato turned over to her and tried to call her down. "Don't worry Rits told me that they fixed the issue."

"And if it isn't?!" Asuka gaze hardened as she couldn't believe this. "What if it kills her?"

Rei turned her head over to Asuka. While it was logical for her to be concerned for her little sibling Rei knew she wouldn't be gone forever. There was a whole tank of clones of her that her soul would be sent too. "It won't matter I am expendable."

Asuka turned to her sister wide eyes and grabbed her shoulders. She knew that Gendo had done a lot of abusive and heartless things but this was just a new level. Her sister just casual said her life didn't matter. "Sis please don't ever say that again your life is not expendable."

' _The sad thing is Rei might be right,'_ Lucy choose that moment to speak as Shinji watched the two sisters. Shinji wondered what Lucy was even talking about. ' _Given how set your father must be on this plan it's likely he took precautions on the change something happened to her.'_

Shinji recalled the tank that Asuka was grown in. It was rather large and if his mother could make a child in it then his father could ensure that Rei wouldn't be lost. At least the part of Lilith's soul that was Rei. ' _She has a bunch of clones doesn't she?'_

There was a low growl coming from Lucy at this. The more they learned about him the more Lucy wanted to rip him apart. Then bring him back only to do it again and again. He will suffer until she broke him completely. Only then will he have her permission to die. ' _Maybe we can have Yui join us I seem to recall she had developed a lot of rage directed at him.'_

Misato decided to get everyone off of this with something else. Although mentally she decided to talk to Rei about her choice of words as well as her sense of self-worth. "Seeing how we need a change of subject Asuka both you and Shinji will be having a Cross Synchronization Test with each other's Eva's."

"What why are we doing that?" Asuka was upset about this. In fact, if she was honest she was starting to hate NERV as an entity at this rate.

"The Commander wanted it to see if any of you could serve as replacement pilots should either of you or your Eva's are out of commission." Misato thought she heard Asuka curse at this. The moment she said 'The Commander' was enough to piss her off.

* * *

Lucy blinked as she reached out into Eva-02. She felt something around them in the LCL. She found herself in a dark room and was greeted with two people. Rather it was one person who was broken in two. "Who are you?"

It was Kyoko Yui's best friend and the mother of Asuka. Lucy had expected something had happened to her but this was extreme. Having her soul split like this was a recipe for problems. Between them, the Progenitor could see the faintest of connections between them. It was slowly trying to merge them back together. "I am a friend." She reached out to this thin connection and on contact pulled on it.

Both halves of Kyoko suddenly felt themselves slam into each other as they screamed in fear. Then suddenly they found themselves as one. Whole after so many years apart. "My name is Lucifer and I am the soul of Yui's son."

Kyoko blinked when she heard that. This was the soul of her best friends child? She looked like some kind of demonic yet sexy woman. Yet, from what she felt when the woman contacted her soul with her own it was the truth. "You're like Lilith, Yui's son is like my daughter."

"Kind of Shinji is still technically human but my body should be seeking us both out." Lucy stopped as she wondered what was going to happen when it did find them. Especially if it managed to enter into NERV and rampaged in their base.

She was pulled out of her hypocritical thoughts by the woman in front of her. "What is going on why are you in here with me?"

That question was easy for Lucy to answer. She took Kyoko hand and showed her. The woman blinked as she became aware of her body. Not her actual one that was dead and long buried. No, the body of Eva-02. " _We are having a Cross Synchronization Test to see if their pilots can pilot each other's Evas,"_ Lucy's voice answered as Kyoko saw her daughter looking on.

It had been so long since she had caused her pain. Since she couldn't hold her anymore. Kyoko wanted to reach out and hold her. She wanted to say she was sorry. " _Asuka."_

She felt a hand on her shoulder as she returned to the soulscape. Kyoko looked at Lucy. "You can still see her if you are willing to be open to her."

With that Kyoko watched as Lucy faded away from her vision. Kyoko returned to viewing the world outside of her from the prison she had been forced into. Even though no one thought it possible a tiny trail of water seem to call from the eyes of the Evangelion.

* * *

Shinji blinked a few times before pulling his hand to his face. After a few moments 'he' let out a sigh. As soon as 'he' did Shinji's voice yelled through 'his' mind. ' _How did we switch places again?!'_

Lucy had no idea how that had happened. It looked like she was going to have to play the part of being her other half again. ' _Honestly Shinji I have no idea.'_

Her first thought was due to Synchronization with the Eva but she threw out both that and the possibility of it being a side effect of contacting the soul trapped in the Eva. If either of them was the case then she should have been in control after the last fight with the Angel. Regardless of this strange phenomenon, they were still in the middle of tests which Ritsuko voice made very clear. "Well, you managed to get a twenty-one in synchronization just barely above the threshold needed to successfully pilot the Eva."

Looking on from the viewing glass Asuka crossed her arms at this. A part of her ego was hurt learning that he could pilot Eva-02, her Evangelion Unit that she trained years for, even if just barely.' _Beginner's luck.'_

* * *

Mari and Kaworu walked out of the Base Commander's office. He had informed them of their transfer to NERV Headquarters. Both Evangelion Units 03, and 05 were to be moved to the Neo-San Francisco port for pick up by the U.N. Pacific Fleet within a weeks time with the two of them being with them.

"You know I heard about the pilot they had at the headquarters," Mari was excited at the prospect of meeting the other pilots as well but the Third Child was the one she wanted to meet the most. Especially given the story about him. "They say that he took on and killed an Angel with no training."

Kaworu had serious doubts about that. To him, it was likely that the Evangelion did it, or he actually did have training. Whatever the case he did wonder himself about the pilots who are defending the Lilin. ' _You know I noticed that Mari been trying to ignore talking about what I told her concerning her new physiology,'_ After he did Mari just choose instead to had back get a drink and from there it seemed she wasn't putting any thought into it. ' _Perhaps on some level, her mind is choosing to block it out?'_

* * *

 **There we go now both stories are even. Man I am going to slow when January comes and I won't love it. If you have any suggests I am all ears to hear them. Oh and should I update this to M rating? I have been thinking of doing so.**

 **Cya all next time.**


	11. Chapter 10

**Ever since this year began I have been writing. I do hope that I can continue this trend next year.**

 **Thank you Scattershot98 for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Asuka got out of the entry plug of Eva-01 with a smirk on her face. She had managed to get more than double Shinji's synchronization score with her Evangelion. Forty-five was more than enough to move it without issue. In his office, Gendo watched the feed.

This confirmed that Asuka connection to Lilith was enough to allow her to pilot Eva-01. As for the other test, Shinji was just barely able to pilot Eva-02. That was actually a surprise. ' _I expected him to be unable to even get an arm to move.'_

Perhaps he was still underestimating his son. Already he had managed to make contact with Yui's soul, defeat two Angels, and pilot an Eva he didn't expect him too. What was going to happen next he found a way to get Yui back? ' _I almost made myself laugh at this.'_

He looked over the latest file he was able to get through a few phone calls. In about a weeks time he was to head to the Antarctic alongside several others. SEELE had, as he expected, listed a spy to join them. ' _The same one I am had ordered to retrieve the embryo of Adam from them.'_

It wasn't like he didn't expect this. Still, this could work out for him assuming he had already retrieved the embryo. He could use this as an excuse to kill him when they set foot on the continent. He pulled up a phone as he gave an order that was relayed through the building. "Ready Eva-00 and have Eva-01 on standby with my son ready for complications."

* * *

Lucy took a breath of the LCL fluid and almost gagged in utter disgust. She knew the fluid was Lilith's blood. She used to bleed the substance herself. She knew that Lilith could survive its removal, hell she herself had to bleed herself in order to help her civilization understand liquid breathing. ' _The only good thing is that we don't technically need it otherwise I would be very pissed.'_

She could almost feel Shinji shuddering at the knowledge that it was actually blood. Given how Eva-00 activation went last time it was decided that Eva-01 would be on standby. As the synchronization rate increased Lucy felt Yu trying to contact them again. She immediately reached out. ' _Shinji Lucy…'_ There was a pause as Yui noticed something was off. ' _Wait why is Lucy in control?'_

' _We don't know.'_ Shinji answered his mother as Lucy looked forward as Rei entered her entry plug.

Lucy while in control of Shinji's body looked at the prototype through the screens. She wondered just which soul was used within the Evangelion Unit. If they needed the soul of a relative then how was Rei even able to pilot it? Asuka was able to pilot Eva-01 due to being part Lilith like the Lilith deprived Evangelion. It was likely that Kyoko was accepting of her and Shinji as such they could barely pilot Eva-02.

As the test began Lucy decided to take no changes. ' _Yui, you want to learn how to project your A.T. field into another to talk?'_

Yui could tell that Lucy was planning something. She could feel it coming off of the ancient being. ' _What do you need?'_

' _Well, I need to check something and Shinji I think this time you are coming with me.'_ As the test began no one notices the low A.T. field reaching out from Eva-01 and into Eva-00.

Lucy and Shinji found themselves with a dark room though this one felt off to the former. She looked around before the answer came to her. It seemed this was indeed deserving of the name prototype. "This is practically just a giant robot that has Angel flesh grafted onto it."

Shinji had a confused look at this declaration. "Isn't that what each of the Eva's are supposed to be?"

Lucy shook her head. She remembered the designs from her time within Yui. This was not like Eva-01 and beyond. "No, with Eva-01 and 02 they are more alive then this thing," Her eyes narrowed. "In fact, I think you could with a few modifications actually turn it into an automatic drone."

Finally, Lucy saw the soul that was within this Eva. Her eyes widened as did Shinji's when he saw what she was looking at. Before them was what looked like four-year-old Rei curled up in a ball and crying. The only way they could tell was because of her facial features as this girl was kind of like Lucy except that her body and even hair was a pure white in color without anything else besides having not noticeable private features. "He didn't," Lucy walked over as her eyes glowed in anger. "He broke off a piece of Rei, a piece of Lilith, and is forcing it into this?"

Once again Gendo dug himself deeper in Lucy's eyes. It made sense why Eva-00 had the potential to go on a rampage. The soul within it wanted to become whole with Rei. The younger version of Rei looked up at them. "A-are you talking about the Commander?" She immediately blinked as she shot up and moved back. "H-how did you both get into here?!"

Shinji walked up to the younger Rei as he put his hand up. "We aren't here to hurt you Rei."

The younger Rei looked at him noticing how he felt familiar. I'm fact, the lady with him also felt familiar. Lucy got down on one knee. "I am Lucifer and this Shinji and we both are two parts of the same soul," Suddenly the four-year-old Rei screamed out in pain as she clutched her head. "What is it?"

"My head hurts please make it stop!" Lucy placed her hand on the fragment head. She understood what she was getting at. The prototype Evangelion was practically torturing her as Rei synchronization score rose.

Eventually, it would rise so high that the girl would do anything to make it stop. This was the source if Eva-00 berserk moments. Lucy and Shinji held the girl in an embrace as the test continued. Shinji blinked as he saw something of a thin thread leading out from her. "Lucy, what is that?"

"I believe it's her soul trying to become whole again," Lucy touched it as she could see that this part of Rei's soul was trying to return to the other Rei. Lucy gripped it and winced in pain. This Eva was growing hostile for some reason. Rei's soul fragment had made it openly hostile to any attempt at fixing this pain. "Shinji help me now!"

He gripped the thread as the younger Rei screamed in pain. Outside Eva-00 began to thrash within its restraints. Eva-01 moved in to help restain it though Yui groaned in pain from trying to keep both her contraction up and hold Eva-00 back from going berserk. ' _Hurry up!'_

As the two of them tried to pull on the thread to get Rei fragment to return to them another presence joined in. The Rei fragment disappeared from the Evangelion soulscape. Lucy and Shinji caught sight of a woman standing before them with part of her body missing. "Thank you for helping her."

As soon as that was done Lucy and Shinji were violently expelled from the Evangelion as You was forced to pull back. The two of them groaned in pain as Shinji blinked a few moments. It looked like he was back in control of his body. ' _This back and forth is getting ridiculous.'_

Shinji gripped his head as Lucy finally pulled herself back up so to speak. ' _Well, Rei's soul back in one piece though what's next did your father imprint his staff with mind control devices?'_

It was sad but right now Shinji could honestly see his dad doing that. Ever since coming here he had only seen what a horrible human being he had been. At this point, he was tempted to join Lucy in breaking his father when this was all said and done. ' _Why who was that woman?'_

Lucy shrugged her shoulders. Before they were expelled she was only able to catch that it was part of a soul and one word. ' _All I could get from her was Naoko.'_

Meanwhile within Eva-00 Rei gasped as she was soon hit with a bunch of painful memories. Each one being of a dark room. The grip of her head and the thrashing about of Eva-00. The last one, however, was shocking. Shinji and some monster woman, an Angel if she could guess. ' _Could this be a hallucination?'_

She placed her hands on her head as the pain told her otherwise. As it subsided a question started to arise. Was Shinji like her and Asuka? ' _Who is Lucifer?'_

* * *

When it awoke it found itself in the ruins of a city. Something built not by its kind but by a distant relative. It was then that it sent out signals looking for anyone to talk to. The faint scream of one of its kind dying caught its attention. It screamed about an abomination that they had made. ' _So they have created a means to destroy us?'_

The Angel of Adam didn't know what to do. Does he go and try to find his Progenitor? If he did awaken didn't that already mean that his Progenitor should have fixed the problem? ' _I can feel a Progenitor signal.'_

This couldn't be its Progenitor. This signal had to be the one from the mother of life on this world. The Angel of Adam paused as he weighed his options. Perhaps they were injured and reaching out at random. If that was the case then there was a chance that it could kill her. It had no idea what would happen but it didn't care. With that, it floated up thanks to its A.T. field and headed off in the direction of the signal.

* * *

There was nothing all around on the barren soil. The water was filled with an almost red primordial fluid. Shinji looked on horrified at the only thing of note. Impaled on a floating black moon was a multiarm giant. From its wound, the last drops of LCL fluid flowed out and into the waters below. Out of his mouth, he heard Lucy's voice with horror. "Hela!"

Lucy flew up as she placed her hand on the Progenitor's face. She looked up at her weekly with tears flowing through her eyes. "Th-they…" Her voice was weak as LCL fluid flew out the corner of their lips. "I t-told th-them it wouldn't work."

With the last of her strength, Lucifer's fellow Progenitor showed her what had happened. A few of her children got too ambitious. They sneak on board her ship and learned what they shouldn't. Unable to truly translate it they ended up believing that if they could force a return and a union of souls that they would be grated godhood. Instead, all they succeeded in doing was destroying themselves and the world.

It had been days but finally the souls within the ocean, within the now primordial soup, had finally destroyed themselves. All that remained was blank slates slowly burning within a dying world. With that, Lucy felt the soul of fellow Progenitor leave its body and join the metaphysical realm. Tears fell from both her and Shinji's eyes before Lucy removed her Spear of Longinus from the corpse.

A few moments later Lucy placed her fellow Progenitor's body on to her ships cross. With her spear wrapped together and the primordial ooze floating into the ship. "I promise you that I will warn the others about this so it will never happen to anyone else."

Flying out of it Lucy looked at the now cleaned would. A testament to folly, to pride, and to greed. The ship moved its course set for the system's star. To burn its, the body of the Progenitor and finally boil the ooze away so that the unfortunate souls can find some form of rest within the next realm.

"That's Instrumentality." He could understand now how mad Lucy was to hear about this.

"This wasn't the last time either despite my efforts," Shinji turned around as he saw a saddened look on Lucy's face. "By the time I got around to it three other worlds had suffered the same fate, two being Seeds of Life and the last being a Seed of Knowledge and at least three attempts have been made since then."

That just sounded so stupid. Shinji just saw the end result of such a thing with his own eyes. "H-how can they do that?" He motioned the memory as the Seed-ship carrying the broken remains of a death world fell into the star. "It's happened four times already and it's always the same!"

"I asked myself that question after the last group nearly succeeded in causing the fifth world to die," Lucy sat down on a chair that appeared behind her as she looked down. Hell, she was lucky as when a group found the information on her ship they immediately questioned if they had it properly translated and abandoned it before the plan could begin. "They keep thinking they would do better and succeed where the others had failed."

Half of the remaining Progenitors had already abandoned their worlds because of this. Even Lucy had debated leaving her world behind in order to prevent it from happening. "My dad just wants to be with my mom and he'll doom the world just to do get what he wants."

"And your grandfather is hoping to become a god along with his friends," Shinji gave her a look wondering how she knew that. "While I was hiding in your mother I kind of learned a few things about her father and well I can say that your family is just one big mess."

At least he wasn't completely insane like either of them. Even if he was talking to the voice within his head. Shinji opened his eyes as he awoke from another dip into Lucy's memories. Turning to his clock he let out a sigh.

* * *

Keel typed away at the computer. Gendo was to head off for their latest expedition to the bottom of the world. A few of SEELE members had begun to debate to do with the interloper. SEELE Two, Four, Eight, and Ten believed they had died and was way of no threat to them. Three, Five, Six, Seven, nine and twelve believed that they were a threat that had to be delt with if they weren't dead already.

The rest Eleven, Thirteen, Fourteen, and Fifteen, however, believed they could be of use for their plans. Keel agreed with all sides to a point. The interloper at Second Impact was a threat and an opportunity. Already, an extrasolar Angel had appeared possibly to locate them. That is if it was of the breed of Adam. If it was of Lilith's breed then they may have another way to perform for Third Impact.

Speaking of Third Impact, already Project Revelation had its first completed success. The labs in Germany were beginning to test out a few frameworks on how to develop S2 organs with tests coming in later this month. It seemed that everything was going his way regardless of the few bumps.

A call got his attention. He answered not bothering to check who it was. "What is it?"

"Tabris has left his place," Keel cursed at this. Knowing Tabris he could have hidden his form into anything making it nigh impossible to locate him. Perhaps he should have taken up the idea to freeze him until he was needed.

* * *

Within NERV everyone worked in the command center as the sensor picked up a large octahedron shape floating to the city. Maya turned over to Misato as the large range scans of the A.T. field gave them a rough image of the Angel. "MAGI confirms blood-type blue it's an Angel."

As talk continued going from the strength of the A.T. field to the evacuation orders Gendo just stared on. A visual of the Angel appeared as it neared port. "Eva-01 and Eva-02 are ready for launch," Ritsuko finished typing away. "Eva-00 Isn't finished with its fitting for combat."

"Then it looks like both Asuka and Shinji are going out on there own," Misato would have preferred it if they had all three of them. If the Angel had waited for just a little longer that might have been a possibility.

Within the Eva-02 Asuka blinked as she thought she heard something within the entry plug. Asuka looked around as she thought she felt something brush right past her cheek. ' _Asuka,'_ Asuka thought she could see her mother for just a brief moment. ' _I'm always with you.'_

Asuka eyes widened as she realized it was her mother. The Evangelions had souls within them like Shinji had told her. Subconsciously Asuka reached out with her A.T. field touching her mother's within the Eva. Outside in the monitoring stations, Asuka's synchronization score began to increase until it capped at eighty percent. ' _Mama, I missed you.'_

' _I missed you two my kleiner Engel.'_ It almost felt cruel to Kyoko being unable to truly hold her daughter even if she was this close to her. To her surprise, Asuka's A.T. field reached into the Eva as suddenly Kyoko was greeted with the projection of her daughter's soul.

Despite the near, all white form, her wings, and nude form without any visible privates, Kyoko knew it was her daughter. The two finally embraced after so many years apart.

Watching in the catwalk Rei felt a tear roll down her eye. She looked at the drop as she rubbed it off her check. For the first time ever Rei wondered why she didn't have a mother. ' _Why am I thinking about this?'_ Looking at Eva-02 she knew the answer. Asuka's feelings for her parent had crossed over to her. Somehow she had talked to her. ' _I…'_

Rei turned away as tears continued down her face. While Asuka felt tears of joy Rei felt tears of sadness. While outwardly she continued to appear stoic inwardly she felt like she had missed out on something. The cover story the Commander used was that she was an orphan. It was only known Rei truly felt like one.

* * *

This was where the signal was coming from. There was nothing but another city a lake and some of the life descended from the rival Progenitor. There was nothing around that showed that the Progenitor was around. Still, it seemed that despite the place looking like it was inhabited there was a lack of inhabitants. ' _It's a trap.'_

It opened its body as its form shifted into impossible shapes. It charged up its energy and just like it thought two of the abominations appeared. " _Burn on the pit!"_

A massive laser was fired at both of them starting through and melting the buildings as it passed right through them. Both Evangelions didn't have time to act before both Asuka and Shinji felt the feedback as the laser struck them. When it was done they both had their armor partly melted and from the screams that the Angel had heard they were down.

" _You know that was just disappointing,"_ I had expected them to come out and put him on the defensive. A titanic fight where it did all it could in order to protect his fragile body. Instead, one blast and they are both down. " _Did they both just appear from underground?"_

Returning its shape back to the floating octahedron form it sent a probing scan with its A.T. field. Reaching down it first found the basic makeup the city concrete, asphalt, mental, and then several layers of armor followed by a large opening. ' _So, there is a base underground that sits just on top of what I am guessing is a Seed-ship.'_

Seeing how there wasn't any way to float into the underground cavern it was going to have to force its way into it. Blasting It with its laser was out as such it was going to have to dig an opening. Floating into the city. It came to a stop and began twisting its bottom point. An improvised drill touched the ground as the Angel began its dig into the hidden base. ' _This is going to take a long time isn't it?'_

Maybe they would try to attack it again so it can find entertainment. Because otherwise, this was going to be a rather boring next couple of hours.

* * *

Gendo looked on at the image of the Angel for a moment and then back at Ritsuko and Misato. The Geofront armor could keep it out for several hours. More than enough time for them to regroup and think of a new plan. "Is there a way for us to break through the Angel's A.T. field?"

This was, of course, the biggest problem. The Angel's A.T. field was according to scans a lot tougher than the previous two and was constantly active. "Nothing we currently have can break through Its A.T. field before it counterattacks."

Ritsuko had gone over it. By the time any of their weapons managed to break through the barrier, it would already have had plenty of time to counterattack. Misato thinking about this had an idea. "Then we will just procure one," The both of them turned to her. "The JSSDF has been testing a particle accelerator for a while now in hopes of using it in some upcoming war if we run it through say all the power in Japan we could punch through the barrier and kill the Angel."

The Commander turned his head over to Ritsuko who was looking at Misato. He took note of her expression. "I take it that Captain Katsuragi plan could work?"

Ritsuko did the math within her head. "If we have the MAGI circulate the shot such a shot could break through its A.T. field and hit the core."

That was great news. Plus, thanks to his authority when it came to dealing with the Angels they could procure the particle weapon without issue. "I want Eva-00 ready for combat and both Eva-01 and Eva-02 repaired for battle," He turned to Misato, "You can have Rei help you with moving the particle accelerator."

* * *

A hand reached out of the harbor pulling itself up and out of the water. The soulless body of Lucifer had finally reached its destination. As it walked, regaining its legs as soon as she got on land, it would feel the signal of Lilith. "Makes sense my soul would want to stay close to Lilith."

Even if the body was pretty much robotic and emotionless it did know the echo of love that Lucifer had for Lilith. Although the actions that Lucifer went about for her did seem questionable. The soulless body continued its walk as missiles were launched out from the mountains aimed at something within the city. A laser was seen passing through them as they blow up mid-flight. The sounds of artillery fired echoed through the air as and a flash of light was seen over the horizon.

Finally, after nearly two hours of walking the soulless shell could see what was the cause of all of this. One of the Progenitor of Life's creations. It seemed to be stationary while it was letting the creations of Lilith attack it. The shell turned her head down before get down on its knee and placing its hand on the ground. "The signal is underground," Looking at the Spawn of Adam and at the near abandonment of the city the shell looked around. "There has to be an entrance to whatever is underground."

* * *

Ritsuko couldn't understand how this had happened. The scans of Eva-02 yesterday didn't show any indication about this sudden development. She did a double check just to be absolutely sure about it. ' _Eva-02 has begun the process of developing an S2 organ.'_

Eva-01's S2 Organ was almost fully developed. It wouldn't be long before it would be able to be piloted without the umbilical cord. Having a Second Evangelion Unit developed one was just amazing. Call her curious but she had to see something. Running another scan of Eva-00 she looked for the organ. ' _Well, it was a long shot given that Eva-00 was a prototype.'_

Still, She had to figure out why they were developing these organs. If they could be replicated then NERV would have a huge advantage in their war with the Angels. As well as when their benefactors decide on whether to dispose of them or not.

* * *

 **If you are wondering it's thanks to Asuka reconnecting with Kyoko that Eva-02 is developing an S2 organ. Anyway seeing as in a few days time we will say goodbye to 2018 I would like to say this to all my readers. I wish you all a happy New Year.**

 **Cya all next time with more.**


	12. Chapter 11

**Tomorrow is New Years Eva. This is the last chapter of the year for any story.**

 **Thank you Scattershot98 for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

 _Pain shot through the stump of her arm as Lucifer watched the severed limb fall to the ground. She looked at her opens as Adam was trying to hold in the leaking LCL fluid from his stomach. The two titans, living gods before the world around them, caught their breath as they stared down each other. "This isn't even your world!" Adam held up his red Spear bringing it down to her. Lucy countered with her own as the two of them continued to clash. "Why are you defeating what is not your progeny!"_

 _A laugh escaped the demonic looking being. Of course, he had no idea. In fact, truth be told they shouldn't have ever met in the first place, Her and her love. "I do it for her," Overhead the Door of the Guf that Adam opened began to shake as Lucifer channel her full power. An A.T. field formed as a solid light construct took the place of her served arm. "So, lay down and die already!"_

 _Lucy reached forward with the arm as she blocked the spear with her own and grabbed him by the neck with her A.T. arm. She slammed him into the ground before Adam removed his hand from his gut and blasted her in her eyes. Lucifer was forced off of him as Adam swung slicing one of her legs off. "It's clear that you are broken and deranged."_

 _Broken, that was what they called her. Her creators, her parents in the lowest terms, saw her love as a problem. She wasn't supposed to force this strong a bond with another of her kind. Enraged at this her A.T. field pushed outwards and effectively knocked him away. "To the pit with you," Her A.T. field created another solid light construct taking the form of another limb this time that of her leg. "Join our dead creators!"_

 _Adam held up his weapon as he looked at her. It was clear from the start that something was driving this Progenitor. Something that shouldn't be felt among their kind for one another. "This world was mine I got here first you should be helping me!"_

" _Like I will ever harm my beloved, besides you're not the one whose progeny rule the world!" As she said that he brought down her hand on him as Adam still healing wound was punched open by the A.T. generated limb. "I come here to finally be with her and you are ruining it!" Her construct arm broke apart and seemed to fire itself at him as Adam's A.T. field blocked it and knocked her back._

* * *

Shinji awoke with a groan as the feeling of being burned still lingered on his skin. He shuddered at this looking around and saw Asuka out of bed in a hospital gown herself. The last thing he remembered was them being launched to the surface. ' _What happened?'_

A painful moan echoed in his mind as Lucy awoke. The feedback she had suffered from both Shinji and Yui was enough to give her a headache. ' _The moment we got out the Angel attacked both us and Asuka with a high energy laser and metals the armor of both Eva-01 and Eva-02,'_ She groaned rubbing her nonexistent temples. ' _Yui was screaming in pain as well and I think the connection may have caused us both to fall unconsciousness.'_

As Shinji was brought up to what was going on Asuka was in thought herself. Her mother was in Eva-02. Trapped within the Evangelion and when Eva-02 was injured she could hear her mother scream. Asuka held her hand over her heart as for the first time she wondered if this was a good thing. On one hand, she got to be with her mother again. On the other hand, her mother felt all the pain was inflicted on the Evangelion.

The both of them turned as Rei came walking in pushing a cart with food on it. Asuka looked at her with a questioning look. She only awoke a few minutes before Shinji and hadn't bothered to ask. "Is the Angel defeated?"

Rei shook her head at her sister's question. Already the JSSDF and the U.N. forces were only delaying the Angel by being as much of a nuisance as they could be. "The Angel is currently trying to drill a hole into the Geofront according to Doctor Akagi we have around eight hours until it breaches the final layer."

Asuka cursed at this. They get defeated and the Angel is still sitting there training to end the world. "Do we have a plan of attack?"

A nod came from Rei. She had helped procure the weapon that they were going to use. Both Ritsuko and Misato had to set it up and that meant that the Angel had to be distracted by continues attacks until they were ready. "Captain Katsuragi has a plan to attack the Angel," She motioned to the food on the cart. "After you, both eat you are to both head to your Eva's and await further instructions."

* * *

At first, the missiles and bombardment was a nice change. After a few hours of this, it finally had enough. As the latest volley came at it three lasers shot out blowing them all up in the sky. Shifting around it pointed at the missile batteries and let loose. Several of them were melted from the heat. " _Finally."_

Far out of the way Misato looked at the latest attack. The sun setting overhead as the Angel resumed it's digging. All around them was cables as the whole of Japan's power was being funneled into the weapon. As she turned back Misato stopped. ' _Wait did I just see something?'_

Taking a look she saw nothing. The woman wondered if the stress was getting to her. She could have sworn that she saw a purple humanoid woman. Turning back into finishing orders Misato was unaware of the thing watching her. The body of Lucifer looked on at the creatures of Lilith as they had begun to make this thing.

On the ground below her was a knocked out passerby. Placing her hand on their head as it needed information. While it didn't have Its soul it could still create an A.T. field thanks to its S2 organ. As weak as it was it served its purpose. They were apart of a group called NERV with a base built into the Geofront below the city.

This one had no idea about Lilith, nor did they understand what the base was even built on. The woman though was a captain. Perhaps as a member of the command structure, she would know about where her soul was. Better yet she could hide within her means of transportation.

Finding the blue car wasn't hard. It being parked outside the weapon they were preparing. A particle weapon that should punch through the Angel's, as they called it, A.T. barrier. After a few moments of thought and weighing of its options the being opened the trunk and shrunk down growing smaller before it entered into it. Closing the opening it waited until it was lead into the base.

* * *

After the last battle with the Angel Shinji was hesitant to put back on his plugsuit. If their plan fails then this time the Angel may make sure to keep them down permanently. On the other side, Asuka stared at Eva-02 lost in thought for a moment. "Can I ask you something?"

Asuka turned seeing Rei looking at her. The two of them stood opposite of each other as Rei's eyes moved to Eva-02. Although it would be more accurate to say she was looking at it because of the soul within it. "What was it like to have a mother?"

Rei's question caused Asuka to stare at her. She actually felt bad as she realized it was probably because of their connection. A bond they both share. "I don't know if I can describe that."

"I understand," Rei could still remember the feeling that Asuka had. Her joy at being with her mother. Walking away Asuka looked on before turning back to Eva-02.

The two almost seemed to stare at one another. Kyoko having seen the exchange between the two of them could tell that Rei was somehow connected to her. ' _She looks a lot like Yui,'_ A thought crossed her mind. If Yui made Asuka for her, both as a daughter and as a means to create a vessel for part of Lilith, then it meant that nothing as stopping her from trying it again. ' _Does this mean that Asuka has a sister?'_

She'll have to ask her when they don't have an Angel threatening them. Though she already suspected her old friend had decided to make another one. Speaking of the girl in question Rei looked at Eva-00. The memories of what she had gone through, what the first Rei who had part of herself tossed into the Evangelion, replayed in her mind. ' _The Commander forced me to endure it.'_

There was a small crisis within her. The first Rei had over the years grew to hate Gendo. The constant torment was enough to make her want to lash out at him. Rei felt herself wanting to grab his neck and strangle him the moment she saw him. Make him feel even a tiny bit of what she felt. Trying to hold back these desires was rather hard for her to do.

Then there were the two questions that Rei had. The first was Eva-00 itself. While her previous incarnations were removed from the prototype it did know that something else was inside it. A fragmented soul salvaged at around the same time as her. Would the soul within it allow her to pilot?

Then there was the question on Shinji and Lucifer. The later felt so familiar yet she had no idea why. She wanted to question Shinji about it but couldn't find the time nor could she bring herself to do it. ' _Everything seemed simple before.'_

* * *

After walking to the site of the weapon the group were briefed by Misato. Because she was the best shot they had Asuka was the one who would be holding the rifle. The MAGI system would circulate when she would shoot given that even the slightest variable change could cause the beam to miss. Eva-00 would be on hand with a heat resistant shield made from the space shuttle parts.

That left Eva-01 in reserve in case things were needed. Yui, Lucy, and even Shinji figured the real reason why they were put in the back was due to Gendo orders. After this both You and Lucy started complaining about the man. ' _You know your husband is planning to cause humanity's genocide just to get to you.'_

' _I know he's literally doing the one thing I didn't want to happen!'_ Yui did everything to subvert it. Asuka, Rei, getting absorbed into Eva-01. All meant to make sure that no one would do it.

Shinji looking over to Eva-00 and hearing his mother's thoughts had gotten him thinking. Rei and his mother did look a lot alike. ' _Mom, you were the one who made Rei body right?'_ You and Lucy were pulled out of their conversation at this. ' _Why does she look like you?'_

Yui didn't answer him. The woman knew that if she did then Shinji would think less of her. Unfortunately for her, Lucy was able to get it right out of her. ' _It's because Yui used her DNA and Lilith's when she made her,'_ Lucy looking even deeper continued on. ' _In fact, her name Rei is what your parents were planning to name you if you were a girl.'_

No, words were said as this information sank into Shinji. Finally, he said the words that were on his mind at this. ' _Is she my sister?'_

' _No,'_ Yui couldn't hide her feelings or her reasons for the girl. Chances are they had already been betrayed by her soul. ' _When I was making Asuka had to constantly fix several mutations and alterations that happened during development just to make her genetically Kyoko's daughter, with Rei I only went as far as to keep her stable,'_ Shame filled her given what she had done. ' _I never planned on treating her as my child in the slightest.'_

That just sounded like something his father would do. Shinji couldn't believe that his mother would just do something like that. ' _She was just a tool to you?'_

Yui couldn't explain it to him. She didn't know if he could understand it. ' _Your mother has a habit of it thanks to who raised her,'_ Shinji's focus turned to Lucy. ' _The thing is she knows she what she was doing and hoped to give Rei the opportunities that she would have as a person even if she couldn't see her a tool.'_

It was getting really creepy how she could just read her soul. Although she was correct. She may never have seen Rei as anything but a tool but even then she knew it was best not to treat her like one. It was always a thing she fought with. ' _Shinji, always hoped you would be a better person than me.'_

He wanted to be mad at her. In some ways, he was but just hearing this. His family was messed up. Lucy told him how his grandfather was planning, his father was just the worse, and his mother was at least aware of the kind of person that she was. ' _Mom…'_

He didn't get to continue as he heard Misato's voice over the speakers. "Everyone in position!"

Asuka looked down the rifle as the Angel was being distracted by another round of missiles and bombardment. Rei stood with the shield at the ready. Hopefully, she wouldn't need it. The MAGI system calculated everything as it Asuka held it steady. ' _I would feel more at ease if we could pull from more then just Japan.'_

The targeting system lite up as Asuka pulled the shot. The particle beam fired into the Angel as the bombardment ceased. There was a scream of pain from it as it's shapes formed around it into several spikes. Blood gushing out for a moment. A victorious smile formed on Asuka's face. Until the Angel started shifting shapes again. ' _I missed?!'_

Said Angel was pissed. If the weapon had moved but an inch to the right he would have been dead. Turning its attention to them it shifted form yet again this time there will be no more of them. " _Die!"_

A superheated laser was fired at them. The outward of it literally boil a nearby mountain down into glass. Eva-00 jumped in with the shuttle made shield as the heat started to melt Eva-00 armor. "Rei!" Shinji jumped in front as Yui forced the A.T. field to its maximum.

The blast ceased for a moment as the Angel needed to recharge. It looked on with satisfaction. " _Taste the sweet release of Death!"_

It fired again. Rei pulled up the shield only for Eva-01 to grab it as she was overwhelmed by the heat. Finally, the cooldown ended as Asuka took the shoot. The blast stopped as the Angel let out a scream. This time the attack had hit its mark. It's body breaking apart as it fell to the ground.

With the blinding light gone Asuka and Shinji finally could breathe. The later cursed as he felt light burns all over his body. The metal plating on Eva-01 slightly melted from the laser. Both him and Asuka looked around for Eva-00. The unit being knocked back with its entry plug steaming on the ground not far from it. "Sis/Rei!"

Both pilots didn't waste any time. Racing to her they both exited their Eva's as Shinji grabbed the burning latch. He yelled in pain before Asuka joined him. "Stop crying!"

The both of them managed to get it open as they were created with the smell of burned blood. Sitting in her seat within the burned blood of Lilith was Rei. The girl looked at them both as she suddenly felt a smile form. ' _They came for me.'_

* * *

Misato sighed as the Angel was finally defeated. The celebration was soon to be cut short as within NERV's parking lot the trunk to Misato's care was torn open. Lucifer's body walked out as it looked around. The Commander of this facility had to have her soul. As she walked out of the lot two Section 2 members almost jumped in shock when saw it. "What the hell is that an Angel!"

Lucifer turned to them. It didn't have time to waste on the grunts. That is until they decided to try to shot at it. An orange barrier appeared as the shots bounced off of it. Very, well if they were going to impede it then it will respond in kind. Racing forward it grabbed on to the neck of one of them and threw it right through the wall. The other looked on in fear running away before he found his leg captured. He was pulled back up and slammed into the wall as well.

As they both lay on the ground a screen was heard as one of the personnel looked at the soulless shell. It looked like it was going to have to fight the whole base just to get what it came for. A minute later a report came into the command room as Maya looked on her face going white. "An Angel has been spotted in the base!"

The responses that brought was instant. Looks of shock and horror formed on everyone's faces. Even Gendo was in visible distress. "Bring up a visual from the security cameras now!" It took a full second before everyone got around to it. Appearing in front of everyone was the image of the footage. The three-eyed humanoid looking in front of it as a bullet bounced off its A.T. barrier. Gendo's eyes widened as he couldn't believe it. ' _This wasn't supposed to happen!'_

Misato suddenly got flashbacks to _that_ day. The day everything on earth changed, Second Impact. An Angel had slipped by without them even knowing. This was it they were all dead and Third Impact was going to happen. "H-how did," She took a step back as despair entered her heart. "How did it get passed the MAGI?!"

Ritsuko and her team checked the systems. There was nothing. No signs of tampering of any kind. The thing just couldn't pick it up. "It must be able to hide it's signature."

This was bad really bad. Gendo knew that it couldn't be allowed to make it to Terminal Dogma. Everything he had worked for could not be undone by this thing. "Lock down any pathways not leading to the cages and get the pilots here now!"

* * *

Shinji couldn't believe what he was hearing. Another Angel was attacking. Just after they had felt with the one that almost fired Rei alive. ' _How did it even get passed the MAGI system?!'_

As panic came over him he saw Lucy standing out the corner of his eye. He blinked as he wondered if that was a trick of his eyes. Then he put it together. The MAGI system couldn't pick it up because of how weak It's A.T. field had to be. ' _It's Lucy's body.'_

It had come to Tokyo-3 looking for him. Looking for the soul that rested within him. The soul of Lucifer, his soul. "Asuka see if you can get Rei medical attention I have to confront Luc-" He stopped himself. "The Angel!"

He raced to Eva-01 ignoring Asuka's screams. As he entered into it he could feel Yui contacting him. ' _It's here isn't it?'_

There was sadness in her voice at this. Lucifer's body had come to take back what was it. The body of her son was just a shell housing its soul. Yui was soon greeted with Lucy within ber soulscape. The purple woman wrapped her arms around her. "No matter what happens I want you to know me and Shinji will still see you as our mother."

Yui returned the hug as Eva-01 moved to the nearest launching site. It seemed that finally after fourteen years destiny was finally calling her son. To return to the source of who he was.

* * *

The plan to funnel The Angel through the base and yo the Eva cages was a failure. The moment it caught on to the fact it started forcing its way through the walls of the base. As of now, it was nearing the path to Terminal Dogma. Gendo knew that this was going to become a last stand. With the order given everyone was to do their best to at least try to slow down this thing.

"Sir, Eva-01 is in route to the cages with Eva-02 falling behind!" Gendo barely cared for this. There was no way they could follow the Angel without ripping apart the whole base. Reaching into his pocket he pulled out his gun.

He didn't expect to use it until the opening of Third Impact. Now it looked like everything he had done was for nothing. Regrets formed in him. He had given everything to get back Yui and in the end, ceased being the man he was. ' _This is how everything ends.'_

As he left without a word Shinji now out of his entry plug looked around for anyone. Any sign that could tell him will Lucy's body was running around. He stopped as he saw Misato with a drink in her hand. Her handgun out as she looked at it. Ritsuko was working as fast as she could to stop the Angel. The woman debated fighting it but so far nothing seemed to work. "Misato where is the Angel?"

She looked at Shinji unsure of what to tell him. The world was close to ending and he was outside of his Evangelion. The only hope they had to stop this. "It's two floors down but Shinji you're." He didn't stop before taking off. "Wait, Shinji stop!"

"Where does he think he is going?" Asuka yelled out as her and Rei who was fighting through the pain walked past her. The two siblings of Lilith didn't know what possessed him to just take off like that.

Shinji raced through NERV headquarters as he could feel where he needed to go. Both Asuka and Rei following him as the sounds on gunshots were heard. A Section 2 agents were seen on the wall groaning in pain. Lucy's body had been here. "Where is it?"

The agent looked at Shinji groaning as he forced himself awake. He pointed to the right weakly. "It was going that way but kid."

The agent didn't even get to finished before Shinji raced off and heading down the way he had shown him. Shinji ignored Asuka as she yelled out to him. After a few more minutes there it was. Lucy's body nearly standing at eight feet and manhandling the Section 2 agents like they were nothing. In front of her, Gendo walked up as Lucy's body tossed one of the agents into the wall next to him.

The Commander of NERV stared into the soulless shell gun in hand. The soulless body opened her mouth and spoke to him ignoring the weapon. "Where is my soul?"

For a moment everyone was taken back by it speaking. Gendo didn't expect this at least. Even though it could speak to them Instead of demanding his surrounded or asking for either Adam or Lilith, it was asking for its soul. "I don't have your soul!"

"He's right," Shinji walked up as the soulless shell turned over to him.

Gendo expression for the first time in a long time turned to one of panic as he watched his son walk up to it. "Shinji get out of here now!"

It was nice to know that he did care. Still, he couldn't run away. Both he and Lucy knew this was coming. Shinji placed his hand over his chest. "The soul of Lucifer is inside of me!"

Lucy's body turned him hand before anyone could act impaled its hand into his stomach. Immediately an A.T. field shot out from Shinji as Lucy's body broke into tendrils of organic flesh. The field reached out and grabbed the tendrils pulling it into him.

When it was done he took several deep breaths. Under his skin, the tendrils pulsed before his A.T. field shot out in full. It passed through everyone, down and making contact with the crucified body of Lilith, and all the way up to the surface and across Tokyo-3. Two demonic wings of light shot out from Shinji's back before disappearing.

Standing in the middle of the room Shinji brought his, or rather her hand up to her eyes. A single word escaped her lips as she spoke with a soft feminine tone. "That hurt…" Unconsciousness claimed her.

* * *

 _Lucifer laughed as her LCL fluid flowed out of her mouth. The latest wound in her stomach threatening to open and remove her organs. Her constructs arm gone along with her last still organic leg. Adam stood over her he too having last an arm much of his side and even his eye but he was healing. "You have lost."_

 _He raised his hand to impale her with his Spear of Longinus. To put an end to her life and send her to the next realm. "Never."_

 _She thrust her Spear upwards and into his chest cutting into his S2 organ. His eyes widened in before she pushed it forward with all she could. "Im-impossible…"_

 _His organ finally gave out and soon a massive explosion ripped between the both of them. When it was done Lucifer was laying down on the frozen ground. Her form smaller than before. 'Lilith if you are awake I'm sorry.' She had to heal but with these injuries, she couldn't risk it. A vessel was needed to house her soul until it could heal properly. Looking to the side she saw one of the Lilithian lifeforms. 'That will have to do.'_

* * *

 **After eleven chapters its finally done. Shinji has been reunited with Lucy in full. Now, I have a question. What should I call girl Shinji? Can't use Rei as Rei is the name of Rei (I regret writing that) so if anyone has anyy idea let me now. As for why he was acting like this in the later part of the story. It was a drive to unite thanks to Lucy**

 **Cya all next time. Happy New Year!**


	13. Chapter 12

**Today is January the first. Happy New Year everyone.**

 **Thank you Scattershot98,** **hornofdesolation, and Guest** **for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Gendo just sat in his office as everyone at NERV scrambled in the aftermath of the surprised Angel attack. The Commander rolled his eyes at this. Everyone thought it was an attack and he had as well. ' _It wasn't an attack so much as reunification with us unknowingly housing its target.'_

When that thing had merged with his son he saw the truth. Being that close to it and being conscious had allowed him to see when it's A.T. field entered through him. Yui's writing on something stopping Second Impact was real. ' _Lucifer…'_

The name wasn't in the Dead Sea Scrolls anywhere. Sure, he knew where the name came from in terms of the beliefs of the world. A commonly used name for the devil. ' _In the same book that calls Adam the father of humanity,'_ He wanted to laugh but much like SEELE, he figured it was due to mistranslations from primitive man. ' _The old men probably know things they aren't telling me.'_

As for his son now turned daughter, at least that how he was calling it, he didn't know what to feel. From what he was able to recall Lucifer soul had passed into him/her when they were conceived months after having hidden in his wife ever since the aftermath of stopping Adam. Considering she had healed her and allowed Yui to survive in the environmental aftermath he felt somewhat indebted to the off-world Progenitor. He winced as he thought about his wife.

Yui had made Asuka, and Rei as well, to prevent Third Impact. A way to ensure that Lilith didn't fall into SEELE's hands. She even knew that Eva-01 would be demanding a soul. Yui chose her own to also ensure that Eva-01 couldn't be used as a means to trigger Third Impact. She was beyond pissed that he was literally doing the opposite of what she wanted. ' _Even if she wasn't all instrumentality will do is obliterate humanity.'_

The strengths didn't cancel the flaws. No, they both canceled each other and on such a scale that eventually everyone ceases to be. There was no joining, no greater consciousness, nothing but a dead world and blank souls. Gendo couldn't take this anymore. In one moment everything he had done was revealed to be for nothing. If anything he was actually making _things_ worse for him. "Damn it!"

He slammed his fist on his desk before letting out a sigh in defeat. His wife hated him, he was running her plans, and he was effectively going to commit the greatest crime in human history. Reaching under his desk he looked at the bottle of sake. ' _I am going to need a lot more than just this.'_

He popped the cork out and went to work on the bottle not even caring about his usual one shot only rule. After he had drunk the whole thing he looked up at the ceiling. "What now?"

* * *

Mari looked all around before turning to Kaworu. For a second she felt something like a rush of water passing through her body. "Did you feel that?"

Of course, he did. It was a Progenitor signal and one which was familiar to him. The killer of Adam had become whole. "It's her," Mari was looking at him confused before he turned back to her. "The being that killed Adam has reunited its soul with its body."

"Wait, you didn't tell me that something killed Adam," Come to think of it she didn't ask much about where they came from. All she knew was that Adam shouldn't have been awakened and that everything after it was just a side effect of some people poking something with a stick to see what will happen.

Might as well be a good as time as any to tell his new sister the origins of life on this any many others. "It wasn't relevant until now though seeing how we are on it I think it's best to tell you how life came to be on this world," Kaworu took a seat as they were both waiting at the docks. Unit 04 was being moved with them both being moved with it. "Billions of years ago there was once a species who were at the time the only sentient race in the galaxy, masters of biological, technological and metaphysical understanding this First Ancestral Race was soon torn apart by itself until they reached a state were extinction was enviable."

To Mari that sounded like the commonly used Precursor Race. An ancient species who laid the groundwork for life that followed them. "Let me guess they sent beings like Adam out to make life on other worlds?"

Kaworu had a nod. "There was fourteen half held the Seed of Life the other half had the Seed of Knowledge each was sent out to colonize there own world."

Kaworu pointed to the workers around them. The buildings and the machines. Creations of the Lilin. "The Seed of Knowledge is the ability to change the works to your will," He pointed towards the ship. "Normally, Lilin can only barely swim in the water and would be able to use it to move but with the Seed of Knowledge they will eventually overcome the obstacle through tests, trial, and error."

That did sum up human civilization to Mari. Always moving forward, creating, and testing in all forms. From basic tools to things like computers all thanks to a drive to make life better. "Those born of the Seeds of Life have the power to naturally adapt to their environment there is no need to build a boat when you can simply float over the water."

As he walked Mari followed. Kaworu was recalling from the information that Adam had concerning the Seeds. It was one of the things that didn't seem to fade with him from his previous self. "Those of Knowledge share a similar design and form with each other, weak and yet familiar to each other as to foster cooperation."

"And those with Life don't have similar forms," Mari was starting to get it. The Angels differing looks and appearances was due to their own nature.

"Yes, each one is a collective in itself not one of many," Kaworu looked back at her. "Though each has a cost for Knowledge comes strive as the drive to create gives each member ambition and with its conflict," Another thing that was true about humanity. A history of conflict, wars, ambitions, suffering. The same power that allowed them to do great things also destroys each other. "For Life the cost is stagnation, there is no need to grow together, no great desires, and only basic ambitions."

SEELE when they were told the difference via their scrolls incorrectly assumed that holding both would eliminate the weakness of each. For a moment Kaworu felt possessed as he spoke recounting something imprinted in Adams very soul. "Having both only leads to eventual ruin as the First Ancestral Race discovered all too late."

"Earth was never supposed to have them both on the same world wasn't it?" Mari didn't need to see to know that he was right. She had a hand over her stomach as she knew that within her the war could continue.

Kaworu placed a hand on her shoulder. He may have only lived among the Lilin for a few days but he could tell that they were nothing like he expected. "The progeny are supposed to be shaped by the Progenitor, the Lilin have grown without Lilith guidance, and you now have Adam's ability to make Angels," He turned to her as a smile formed on his face. "Perhaps there might be a chance of peace between the Lilin and the new Angels within you."

* * *

A moan escaped her lips as she was opened her eyes were greeted to the medical ward ceiling. The memories of what happened played in her mind. As soon as she saw Lucy out the corner of her eyes she became almost possessed by the desire to reunite. Her hand moved to her stomach were the hand had pieced and where the body had entered her.

A blush formed as Shinji was aware of the changes to him or rather her. First were her slender and curvy body and her chest. Her breasts were rather, developed for someone her age, even bigger than Rei and Asuka's. The next thing of note was her hair. Somehow it was way too long. It went past her knees for crying out loud. Getting out of bad she noticed her shapely legs causing her blush to deepen. That and a certain part of her to hardened. ' _Wait why do I still have that?'_

Shinji was reminded when Lucy had asked him how she, then he, felt about being a hermaphrodite. It seemed she was being serious as now here she was. Reaching down she decided to see what changed. ' _I only have the meat stick and the feminine parts…'_ Though knowing what she was now that probably was just on the surface. ' _What do I look like?'_

Finding a reflective surface she was given her answer. Her appearance was similar to her mother's. Her hair had grown a bit lighter in shape and her irises were now a dark yellow like Lucy's had been. Raising her hand up she saw her fingernails tipped almost like claws. Tapping the metal they seemed to dig in and with a small swipe, a scratch formed. Shinji continued to look on in surprise before a voice caught her attention. "You're up."

Turning around Shinji was met with Rei who looked at her. The two stared looking at each other. Yui's words on Rei were still fresh in her mind. The girl was made with her mother's DNA. Yet, Yui only stabilized it enough so she didn't break apart leaving all the mutations. "Yeah," Shinji blinked at her soft feminine voice. ' _I really am this aren't I?'_

"You are like me and Asuka," Rei's words were more stating of fact than anything else. She was right after all.

"Kind of," Shinji looked at her as she felt herself want to pull her in. She could see what she assumed was Lilith in her place. Shinji could feel the love Lucifer had for her and the desire to kiss her.

Rei herself felt heat rising up in her. Staring at the now changed Third Child was being something up in her. It was like something within her was telling her to wrap her arms around Shinji. "Kind of?" The both of them were cut off when Asuka looked at the new Shinji. "I want answers."

The whole base was still in an uproar about the surprised Angel attack. At least that what they thought was one. The MAGI system couldn't figure out what had happened after the merge. The blood type was orange which meant that the system couldn't confirm it either way. "I believe we all do." Ritsuko voice caught them as she along with a group of Section 2 was behind her. "However, until we can concern what happened Shinji," She looked at the now turned girl. "Will, remain here to see if the contamination is a threat."

That did not sound like she was going to enjoy this. Both Rei and Asuka walked out as Ritsuko stared at the transformed girl. Gendo while currently in his office had given an order to call him when Shinji awoke he was currently suffering drunken effects. This left Ritsuko to look at the boy turned girl with a mix of suspicion and curiosity. Perhaps it was time for a few tests.

* * *

Genetically speaking Shinji was similar to Asuka and Rei. The Angels DNA having spliced itself perfectly into her body. Unlike a hypothetical infection, this seemed like the DNA was made for her. ' _Gendo did say that that it was after it's soul.'_

Her, Kozo and Gendo were the only ones besides Asuka and Rei to know if the exchange. Their Commander had let them in on the fact that Yui talked about a being stopping Second Impact in her notes. If that was indeed the being in question then what did that make the Third Child? ' _A vessel like the First and Second.'_

There were other changes to the body besides just her gender. The first was an S2 organ that unlike the last medical scans of the two Lilith vessels was active. This meant that Shinji should be able to use an A.T. field of an unknown strength level. The second was the internal structure of her reproductive organs. She had the basic structure of everything a girl her age should have but she also had some of the glands that a male would have. Her ovaries, slightly bigger than normal, seemed connected to them and to the masculine organ.

Looking through a microscope she was greeted with the appearance of sperm cells swimming around. Shinji was rather hesitant to give her a sample but after some mild cozying and s bit of a threat, she produced the sample. "She's a biological hermaphrodite."

Speaking of the girl in question seeing how she still had Shinji's brainwaves and showed no threat to her as they did the tests Ritsuko felt it was best to declare that she was safe. The only problem was now getting her new clothes. Her old ones were no longer suited for her. Currently, Shinji was wearing the girl's school uniform along with a pair of bra and panties that would fit her that they had on hand.

' _Lucy are you there?'_ Silence was all that greeted her. Not once had the voice that been with her on and off across her whole life replied since she had awoke. ' _Did she disappear?'_

As she thought about this she looked at her long mane of hair. She could really use a haircut. "Well, Shinji the only thing that remains for you is to see if you can still synchronize with your Eva," Although that might not be a problem. If Asuka and Rei could do it then she could as well. "Now, when you leave this room you will not tell anyone who isn't already informed of how you transformed ok."

Shinji didn't need to be told twice. Everyone was still jumpy about an Angel getting into NERV. The official story was that the pilot had done something that allowed him to kill the Angel while being turned into a girl. Either out of relief or some strong convincing everyone seemed to just buy it. "Can I get some scissors first?"

Half an hour later Shinji threw her arms up in defeat. No matter how many times she cut it the hair would just grow back right before her eyes. At the very least the hair in front of her head remained in a bob cut. She looked at the mound of hair on the ground around her. "Fine, I'll just wear my hair long."

Ritsuko who was watching this made a note to burn the hair for later. Still, it was amazing to see an Angel's regeneration factor working in such a short time frame. "I'll see about getting you some extra time in the showers and a special comb to help get the LCL fluid out," Thinking about it she might as well get one for each of the pilots. "I'll have to make some adjustments but we do have a plug suit that might fit for you."

* * *

Yui looked at the two Evangelion Units before her. She hadn't tried to make contact with each soul within them. Know that she did know how perhaps she could change that. It beat just being alone to herself. Reaching out to Eva-02 she readied herself to see what state Kyoko was in. ' _Hello?'_

There was a moment of silence. Maybe she couldn't do it like she thought. As she was about to pull back she was finally given an answer. ' _Yui is that you?'_

The two stood in a dark room. A projection of what was happening caused by their souls. Kyoko looked at her friend before wrapping her arms around her. "It really is you I thought you had died."

In a way she did. Her body had been lost and now all she was is inside of Eva-01. "The experiment didn't kill me but Eva-01 took my soul."

Kyoko shuddered at this. Eva-02 had taken half of hers while the other half was tossed into it at a later time. At least she was whole again. "So, how are you speaking to me?" Kyoko stopped as she realized it had to be her son or rather the thing within her son. "You learned this from Lucifer?"

"Yes, it's a thing where I project a certain A.T. field to a person and talk to them in a sort of telepathy," The real thing was more complex but it basically was as she said. She looked at her old friend noticing how like her she didn't seem to age. Perhaps this is what souls generally are? "It was a surprise to learn that my son was like Asuka."

Kyoko gave Yui a serious look. There was one thing on her mind right now The weird blue haired girl that her daughter seemed to have a connection too. One that looked suspiciously like Yui. "Yui, does Asuka have a sister?" Yui was taken back by this. "I saw her that girl that looked like you."

"You saw Rei?" Yui had already had a conversation with her son about this. Especially concerning her lack of care for the girl that she made. "Yes, she is made from Lilith as well."

Kyoko could see that Yui was distress by this. She tried to reach out to her but Yui turned away. "Kyoko you know when I made Asuka for you I…"

Suddenly Yui was forced back into her body as a small surge of pain shot through her being. Apparently, she couldn't hold that for long without being drained in a sense. ' _Kyoko, Asuka,'_ She paused as she thought of the girl that she had left to her husband. ' _Rei I'm so sorry.'_

* * *

Misato looked at Ritsuko as she stood in front of Eva-01. She had been rather worried about Shinji after seeing the now transformed girl in the hospital bed. When Asuka started to complain about being unable to speak to her Misato knew that Shinji was awake. "You're having Shinji do a synchronization test after what happened?!"

Ritsuko turned to her with a simple nod. "Of course, given Shinji's sudden change it best we see if she can still synchronize with Eva-0," The faux blonde turned her head to the side the girl in question finally walked up to them. "I mean look for yourself she fine."

Shinji was kind of having some trouble with her new plugsuit. True to Ritsuko word it did need some modifications as it was hastily made. Her waist felt rather tight and it did squeeze over her shoulders. It did, however, draw attention to her chest thanks to it being a lighter shade of purple over her breasts. "This is a bit tight around my shoulders and waist."

The scientist made note of this. A few changes were needed to be made for her but overall it fit. Misato looked at Shinji with worry on her face. Like nearly everyone she had known that the Angel had done something to him before it was defeated. "Shinji, I have to ask how are you dealing with you know."

Shinji shrugged her shoulders. It was strange how quickly she was just accepting her new change from male to female, or rather a female hermaphrodite. Although given that Lucy was visibly female herself that might have explained it. Whatever the case Shinji didn't feel _**all**_ that different. "I've accepted it," She looked down at herself. "I mean I am kind of stick now being almost girl."

"Almost?" Ritsuko whispered into Misato's ear about a certain biological change. Misato had a slight tint of pink to her checks at this. "Oh, well that is something for whomever she gets with."

The girl in question really wished Misato wasn't here right now. Shinji knew that this could lead to a whole different bount of teasing. A few minutes later she was within the entry plug as the test began. Subconsciously she reached out wondering if her mother was here. No response came as Yui just looked at her turned on keeping a distance.

Watching from the computer screen Mays looked at the number with a frown. The boy now turned girl synchronization rate was down resting at just about fourth three percent. "Shinji's sync rate was almost at a hundred and now it's less than half that."

There were several factors for that. The mental changes from altering gender were the first one to come mind, followed by her genetic alterations, and perhaps even changes in Eva-01. ' _Perhaps Yui is having s hard time seeing her as her son, we daughter.'_ Regardless as the test continued her score showed no sign of increasing. "Alright, Shinji that's enough."

At the very least it was possible for Shinji to pilot Eva-01. That was one of Ritsuko's biggest concerns. Misato looked as she got out of the entry plug with her whole hair practically dripping with the LCL fluid. "She's going to need a haircut."

"Already, tried it just grows back until it reaches its current length." Which reminds her she had to burn the pile. Although she did wonder with Misato was going to try and see if she could prove her wrong.

* * *

In a secure location, an 11 appeared on a computer screen. SEELE member Eleven as they were know. The computer was equipped with a one-way camera as the member of the very real secret society that controlled much of everything looked at the sleeping scientist. "Doctor Hawkins asleep I see."

The doctor in question awoke with a freight. Falling out of her seat she pulled herself back up. Annoyed by being brought out of her dream. "I don't know what time it is for you in Japan but its the middle of the night here in Iceland!" She really hated being assigned here. After Second Impact Iceland was rendered a wasteland by the global effects. It was official under the U.N. Which made it the perfect place for SEELE to store some of their secrets. "Wait, we are you calling me?"

"Your report, you believe you might have been able to pull information from the salvaged White Moon's systems?" She gave a nod as she turned over to the pieces that SEELE was able to get from the first expedition after Second Impact. On first glance, much of it seemed like rock and maybe some kind of strange bone like coral. In actuality, it was a kind of pseudo-biological machinery.

SEELE had been trying to get information out of it even as their focus turned else were. With the confirmation of an interloper and Tabris disappearing it became more paramount that they find out anything useful. "I believe so let me see," She hadn't tested this. ' _No time like the present.'_ A few moments nothing happened. "Come on you stupid thing…" Finally, something came on the screen. "It works!"

SEELE Eleven couldn't show it but this news brought a smile to their face. Who knows what secrets could be found from this. "Very good Doctor continue your work and you will be rewarded handsomely."

* * *

Kaworu sighed as he stood onboard the deck of the aircraft carrier. They were leaving port in the morning. Heading for Tokyo-3 and NERV. His mind turned to what he had said to Mari. As Adam, he didn't think peace was possible. As Tabris he had seen that the Lilin were not as he thought, and as Kaworu he now believed that peace was possible. ' _For that be achieved my children, my siblings, have to die.'_

That was a rather sober thought but a necessary one. Adam had imparted on them the desire for war with the Lilin. It wasn't done out of malice or hatred but out of ignorance and out of the idea that it was enviable. ' _I do hope that the other one won't kill us when we meet again.'_

* * *

 **Now seeing how I haven't gotten any names I will be using Shinji for the time being. When I do have a name I will tell you all either in the story or via author notes. As for updates this month might be rather slow in that regards. I apologize to everyone. I also am looking to update my other stories.**

 **Cya later next time everyone.**


	14. Chapter 13

**Morning everyone. So before we begin yes this update is three days old. I said it before but this month I am slow on updates. My apologies.**

 **Thank you knight7572 and Scattershot98 for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Shinji stood in front of her father's desk. With him finally sobering it up he had called for his son now daughter to came to him. There was an awkward silence as Gendo stared at her. Unsure on what to do. Much like Rei, she seemed to appear a lot like Yui. Thinking about his wife only lowered his mood. "Should I address you as Shinji or would you prefer Lucifer?"

Hearing this caused Shinji to wonder about what she should be addressed as. Technically she was Lucifer. The body and soul reunited in a new form. But she was also Shinji a fourteen-year-old boy who spent much of his life in a state of quiet sadness. In a way, she wasn't either of them anymore. "I think Shinji is fine for right now."

There were so many questions he wanted answers for. After several moments he finally settled on one of them. "Did you always know?" This one was a more personal matter to him and probably Yui. "What you were?"

"No only until after I got to Tokyo-3 after I piloted the Eva and blacked out." Shinji was starting to feel a bit of an identity issue. Gendo's question and her inability to speak to Lucy made her wonder if both Shinji and Lucy were gone and whatever she was came about because of it.

While she had a crisis of identity Gendo was having his own crisis. Just looking at Shinji made him question their relationship, or rather what could pass as one. He had no illusions that he wasn't a terrible father. Leaving your son at a train station because you couldn't see yourself raising him was to many a sign he shouldn't be one. This just made it even harder on him. "Does your mother know?"

Even saying that just sounded weird to Gendo. Shinji gave him a nod in confirmation. "She does."

At this point, Gendo wouldn't be surprised if Yui always knew. If the reason she made him promise was to protect the vessel for Lucifer's soul. Sure, Gendo didn't know that it was also a surprise to her but given everything else he was willing to believe it. "Very, well if you have any issues with your new form Ritsuko should be able to help you," As for the issue of ID Cards he was going to have to get a new one for her. "You are dismissed."

* * *

Rei sat on the bed that she and Asuka shared as she thought about herself. Now that everything had calmed down she finally had time to herself. Ever since the fragment of her soul representing the first Rei returned to her she felt conflicted. Her first self was much like her current self accepting of her roll in the scenario. At least until she was left in Eva-00.

The prototype wasn't like the other Evangelions. The truth was it had been salvaged and put together using parts from each of the failed Evangelions within the graveyard. Machinery was used to fill in any gaps and allow the organic parts to function. A Frankenstein's monster was the best description of the thing and being inside it. Rei gripped herself. ' _I didn't like that.'_

That was where the hate for Gendo came from. After so long within it, the fragment came to utterly hate him. It's first attempt at a rampage when she had gotten hurt was her attempting to find and hurt him. "The Commander never cared for me."

Placing her hand on her chest she recalled the feelings that she felt from Asuka. The joy and happiness of seeing her mother. It was then that Rei knew what being an orphan was. The moment she was removed from the tank she wasn't cared for her like her sister.

Asuka was handed to Kyoko to be given as a child for her. Kyoko embraced it and Asuka saw herself as her daughter in full as well. Rei was artificially aged into being a few years old. She was never meant to have anything of a normal childhood. ' _Or was I?'_

Yui had made her originally. She didn't know but she was certain her clones only existed because of the Commander altering something to spark the development of them. As she thought of it the more the feeling of anger about him returned. ' _Was I originally supposed to be like my sister and grow up as someone's daughter?'_

The thought of growing up with a mother or a family passed through her mind. A little daydream of her having a parent who loved and cared for her like Kyoko for Asuka crossed through her mind. The fantasy only served to feed her anger. In that one moment, Rei could see that her first self had a point in disliking Gendo.

* * *

Shinji walked into the apartment with Misato following behind. Pen Pen was first to greet them and looked at Shinji in confusion. The rather intelligent penguin couldn't put his flipper on it but the female in front of him felt familiar. Seeing his confusion Misato decided to explain it to him. "Pen Pen there was an accident at NERV and now Shinji here is a girl."

Pen Pen looked at the now changed girl with a bewildered expression. At least that's what it seemed to be. Asuka made herself known as she looked at the now girl. "Yes, an accident with him killing the Angel."

Asuka was there and saw it. The Angel wasn't defeated. No, instead it had come looking for Its soul which happened to have been within Shinji. While the Commander made in very clear that no one was to talk about it and made up some stupid tail about it being destroyed Asuka wanted answers. Shinji was terrified of facing her right now.

At that moment Misato let out a loud yawn. She had been up for almost two days now and it was starting to get to her. "Well, I think I need to check into bed just don't do anything loud alright."

As she walked past them Shinji felt like a deer in the headlights. She didn't want to be left with Asuka especially given the way she was looking at her. ' _It's kind of cute actually.'_ That did not just cross her mind. "S-so, you w-what answers?"

"And I am getting them one way or an another."

* * *

When was the last time he had come down here? Gendo stood in front of the LCL lake and the figure that had been crucified on the red cross. Lilith the Progenitor of all Lilithian life. He had thought that he would be down here to have Rei, and later her and Asuka, return to Lilith to give him back his wife. How foolish was him to think that when the outcome would just be pointless destruction.

A new scenario was needed or rather a new outcome. Instrumentality was off the table. Instead of having thought about it the process might not be needed anyway. He truly didn't know why but he felt like information had been unknowingly parted on him at what they could truly do and the options that exist. "I wonder if there is still anything inside of you?"

He knew the answer and even then he still couldn't believe that such a being could fit inside of Shinji. That wasn't how metaphysical biology worked but as far as he knew maybe that was it. Kozo was more of an expert than him. Continuing to stare at the body of Lilith an idea crossed his mind. Perhaps it was best to return them both to Lilith when all was done anyway. No to cause the Third Impact SEELE or he had wanted but instead to put an end to SEELE, get this wife back, and possibly fix the world.

There were other variables to deal with. Adam was one of them. The embryo was to be handed to him. A question on what he was going to do with it arose. He stopped as his phone started to ring. It was exactly surprising that he could get reception this far underground. "Hello?"

As he talked unknown to him the being crucified before him was aware of his presence. The feeling of the familiar touch of _her_ A.T. field had brought her out of the deep coma and into a state of aware dreaming. " _Lucy…"_

Lilith could see out two other pairs of eyes. The names Asuka Langley Soryu and Rei Ayanami echoed in her head. These along with Lilith were her names. Each one a part of her. Looking through the eyes of the piece if her named Asuka she saw one of her, no she saw _her_. Somehow Lucifer was here and in a form like that of her pieces. She was talking about how she ended up on here. " _My love."_

* * *

Asuka looked at Shinji as the words about her finally set in. Lucifer a Progenitor like Lilith had come all the way to earth searching for her. "So, why exactly did you, her, you know what I mean," This was kind of confusing the redhead. "Come looking for her?"

A blush formed in her face. Shinji looked away as the kiss that Asuka gave her when they first met replayed in her mind. "She came because the two of them were in a relationship and she wanted to fulfill their promise to get, well," Shinji looked at her as she managed to swallow her fears. "Married."

There was silence as Asuka mind recalled the flash of memories. The promise that Lucifer and Lilith made. A forbidden love that shouldn't have been. Before Asuka knew it she pulled Shinji to herself and kissed her. As this went on Asuka felt a strong desire, longing, and above all joy at feeling her lips. Shinji, while surprised by this, returned the kiss anyway as the two of them continued to kiss. When Asuka pulled back she whispered in an unknown language that Shinji could understand. " _It's been too long Lucifer."_

Shinji looked at Asuka's, or rather Lilith's, loving eyes. As soon as that happened Asuka blinked as she wondered what just happened. "What the hell just happened?"

"I think that was Lilith," Shinji was actually amazed that that had just happened. After a bit of thought, it made sense given that the relationship between her and Lilith was likely the same as with her and Lucy.

Asuka, while surprised by this, placed her fingers on her lips. The feeling of kissing Shinji was still fresh in her mind. ' _It was kind of nice.'_ She felt a gentle hand pushing her to forward even though no one was physically there. Asuka looked at the girl below her. "You said that Lucifer and Lilith were planning to get married," Her expression was unreadable for a moment. "Does that mean you feel the same to me and Rei?"

When she tried to answer Shinji stopped herself. A blush formed as she suddenly thought of the three of them together. If she said that then would Asuka attack her? "I…"

She was stopped from talking as Asuka placed her hand on her lips. The redhead had already made a decision about this. These feelings were too strong to ignore. "We can be in a relationship but marriage is a bit much," Personally as much as a part of her, likely the feelings from Lilith, wanted Asuka was a bit too young for that. "Just don't think I'm doing this because Lucifer and Lilith had one alright."

By the sound of it, Shinji wondered if Lilith did have a hand in it. Although when they did meet Asuka did kiss her back when she was a boy. A kiss that she had always enjoyed rather heavily. Maybe it was just inevitable that they would fall in love with each other? ' _We are Lucy and Lilith.'_

"Now, how about you make us dinner?" Asuka was really hungry and she rather not have taken out right now.

* * *

Back in her place tears formed in the eyes of Lilith. They were a mix of joy and sadness. After so long it seemed that they were finally able to be together. The sad part was that Lilith had pictured it being something else. When they both set off Lilith had pictured that both of them would one day meet with their creations following behind them. Finally with their tasks done they could have the relationship that their creators discouraged.

Instead, she learned that she had crashed into this planet and was unable to help her children. The Lilin as they are were not what she had envisioned. Maybe it was due to her not being around to guide their evolution letting random mutation do the work. Sure, in the end, they had the basic form but there was a lot that could have been. Longer life spans, better healing and immune system, and as for the females of the species… ' _Why must childbirth be so painful for them along with these periods?'_

If she had been around it would have been a truly wondrous thing for them. Something that she wanted to have herself. The progenitors were not made with it in mind. Technically, in a way, all life on earth was her kids but Lilith wanted to have what many of them had. " _Can I have it now?"_

Both Asuka and Rei were her. Eventually, when all was done she would have to take them back. Although, perhaps instead she could reverse the process and let Rei and Asuka assimilated her. This way she could finally have the means to give her what she desired about all else. ' _Babies I can finally have babies of my own to hold in my arms.'_

Anyone reading her mind would call her baby crazy. The thing is she wouldn't deny that she was. Reproduction always was the subject of evolution that she took an _unhealthy_ interest in. At least her creators called it unhealthy. Just as they saw her relationship with Lucifer as unnatural. ' _At least I won't have to hear from them anymore.'_

* * *

Misato couldn't believe what she was reading. The JSSDF was going to unveil a new robot that they claim would be a substitute for the Evangelions. The designer of the robots, The Jet Alone Project, seemed unwilling to comment on it while the company making the robot seemed to boast about it. Ritsuko found it almost funny. "Really, they think a bucket of bolts can defeat the Angels."

"Aren't the Evangelions robots?" Misato didn't have the clearance to know the truth of the Evangelions. Like so many they just thought it was robots. Although the rumor that they were alien technology did exist.

Ritsuko cursed herself for letting that slip out. For a moment she thought about what to say but then she remembered that the Commander wasn't here. Her office didn't have recorders and seeing how she was doomed anyway she might as well tell her. "Misato what I am about to tell you is something you can not tell anyone under any circumstances."

She knew when to keep her mouth shut. Whatever Ritsuko was going to tell her was something that the doctor shouldn't be telling her. ' _So, the Evangelions are alien technology.'_ Misato wouldn't get that far ahead of herself. "It's about the Eva's isn't it?"

A nod of confirmation was given before Ritsuko turned on her computer. After several passwords, she showed her an inner schematic of Eva-00. Looking at it Misato's eyes widened as several of the parts were listed as organic. "The Evangelions are actually organic beings we fired with cybernetics and metal plating."

Misato looked at the next one for Eva-01. Unlike Eva-00 which seemed more machine-like Eva-01 had a completely organic body and core. At the sight of a developing S2 organ, Misato knew what this actually was. "They're Angels?!"

"I believe you can call the false Angels," Ritsuko knew how much Misato disliked Angels. The trauma of Second Impact causing it. For a moment she wondered how she would feel of having three half Angels, including the likely reborn one that stopped Second Impact. "Each one is made from cloned tissue and then the mechanical parts are added on, with Eva-00 being the opposite as is its made from salvaged organic parts from the failed Evangelions held in a mechanical frame."

One of NERV's greatest secrets were now before her. The Evangelions were able to fight Angels due to being in a sense ones themselves. "B-but what would happen if one of them wake up and decide to destroy the world?!"

Misato couldn't believe how reckless this was. She was suddenly worried for the pilots. They could be changed by this. Everything about this was wrong so very wrong. "The children could this change them?!"

Ritsuko looked at Misato who was worried about the children piloting. The thing is there was no proof that an Evangelion would change its pilot. There was also the fact that the three of them were currently Nephilim, part Angel themselves, though telling Misato that would probably be a danger for the pilots. "Don't worry we have enough data to know that could never happen."

* * *

Mari was bored out of her mind. Who knew being on a warship could be so boring. She wanted to use her powers to elevate said boredom but Kaworu made it clear that wasn't a good idea. With nothing to do she decided to just stay in the quarters that she was given. With nothing to do she started to think about the future concerning herself.

' _Ok, so what am I going to do about all of you?'_ She placed a hand on her stomach and thought about the whole fact that she was now an Angel factory. Kaworu words on peace being possible did make her hopeful but on the other hand, she wondered if it was a good idea to eventually come out with it. ' _Eh, I'll burn that bridge when I come to it.'_

Pulling out her laptop Mari began to look over a few of the online forums. On the news there was a story on the rising warlord in Africa, India continuing to recover from its nuclear war with Pakistan, China trying to project it's authority again while everyone around it in the South China sea opposing it including members of the U.N. There was almost nothing of note except the JSSDF revealing their new plans for a giant robot. ' _The world we live in were now giant robots are a reality.'_

Honestly, a part of her wanted to see how well it did against an Evangelion or even an Angel. Thinking about it she did wonder if NERV would try to sabotage it. To Mari, it seemed like such a waste. Typing away she looked at a few things that caught her interests. A knock caught her attention from the boredom of looking at her computer. "Come in."

Kaworu walked into her quarters as she was randomly searching the internet. Seeing how she didn't seem to walk out of them all day Kaworu decided to check on her. "You know I almost expected you to come by to at least eat."

He got a shrug from Mari at this. According to him, her S2 organ allowed her all the energy she needed. The strange organ was explained to be something of an evolutionary marvel. Something the First Ancestral Race developed from fusing their advanced knowledge of genetics and metaphysics. "I don't really feel hungry anymore, or all that sleepy."

That last part was also due to her new organ. Apparently, while they do sleep it's more of a means to hibernate for periods and recover then actual biological need. Although Kaworu did it more because he enjoyed the peace. Even once learning how to remain aware while doing so. "People will get suspicious of you if you don't eat or sleep in a somewhat regular schedule," He handed her some feed from the ship's rations. "Personally I find joy in the acts even if they are unnecessary."

Mari did admit she was starting miss the taste of her favorite foods. Taking the bag out of his hands she took a bite if the cooled food not really caring that it was unneeded. ' _I think I might be accepting my new nature a bit too much.'_

* * *

SEELE Eleven looked at the information that their good scientist had gotten. The first thing was a list of names. Fourteen of them with both Adam and Lilith listed on them. After a bit more digging through the data banks, it was then revealed that these were the names of the Progenitors fourteen beings were were tasked by their creators to spread life to fourteen colonizes. Seven of each were divided between Seeds of Life and Knowledge along with them being placed based on age.

From this, the oldest was Shiv, a Seed of Life Progenitor, while the youngest was Lucifer, who like Lilith was a Seed of Knowledge Progenitor. According to scans from the White Moon, it believed that Lucifer was the one who killed Adam. ' _This is a surprising boon.'_

There was practically another Lilith somewhere in the world. If they can get their hands on them then they won't need Lilith. There was still more coming from the computer systems but right now SEELE had to be informed about Lucifer. Plans were going to be needed and they had to locate her body and or soul. Tapping on a keyboard a secure channel opened up between them and SEELE One. "The data extraction was a success I am sending you a copy of it right now."

A few minutes passed as SEELE Eleven awaited a reaction from SEELE One. On the other end, Keel looked at the information unsure if he should be worried or if he should feel something of joy at this. If one of these fourteen had suddenly appeared then more of them could follow. However, the one that they know knew of was like Lilith. "I'll talk to the rest of the council about this."

* * *

On t.v. the news went on about the first tests of the Jet Alone Project. Sitting at a bar the designer of the robot looked on with anger at this. The idiots choose to alter his designs several times. Then when he refused to help anymore they tossed him aside and went ahead anyway. ' _Oh, no they didn't tell me that it was meant to create an alternative to the Evangelions.'_

Maybe he should have taken the offer from either the Russians or the Americans. At least they would tell him if any changes would be made and why. A glass of grape wine was dropped next to him. "I didn't order this."

The bartender just lazily looked up at him before pointing to one of the tables. "That guy ordered it for you go complain to him."

Sitting alone was a shady individual. His appearance was hidden over his trench coat, hat, and sunglasses. Getting up from the bar he took a seat across from the guy. "So, who is it then?" He knew that it had to be one of those people. "The Americans, Russia, Germany, or are you with the JSSDF?"

The man merely chuckled at this. His employers were right in saying that this man had been sought out before. "I work for a certain group within the U.N."

This was a surprise. Thanks to NERV being technically apart of the U.N. oversight he didn't expect them to come wanting designs for giant robots. "I have nothing to lose at this point."

* * *

Gendo looked out the window of the plane for a moment. He was being flown to New Zealand there to meet up with the rest of the expedition and set off for the broke continent at the bottom of the world. His first thought was to find the Spear of Longinus that Lucifer had. From the few memories of that fight, he was able to see he knew that the object was likely still resting on it.

There was also the issue of the spice who was supposed to hand him Adam's embryo. What was he going to do with it now was something even he didn't know. Instrumentality wasn't an option that would lead to anything, and he couldn't well let one of the Angels or SEELE get it. ' _Destroying it just seems like a_ waste.'

* * *

 **You know, looking back I noticed a lot of good Evangelion stories that are incomplete. I bring this up because I would like to see them continued in some form. Now, I'll let you in on a little secret. I have two paths for where this story will go. All of which depends on a certain thing happening or not. Right now I am not planning on following either one just yet.**

 **Cya all next time.**


End file.
